From 5f48e864277c8bbdf9c86a2dc0dcb1ae2deb0f9d Mon Sep 17 00:00:00 2001 From: Claire Rioualen Date: Thu, 29 Feb 2024 17:56:39 +0100 Subject: [PATCH] new test queries notebook --- src/webapp/test_queries/test-queries.ipynb | 18318 ++++++++++++++++++- 1 file changed, 18181 insertions(+), 137 deletions(-) diff --git a/src/webapp/test_queries/test-queries.ipynb b/src/webapp/test_queries/test-queries.ipynb index 5efc8f7..72fb342 100644 --- a/src/webapp/test_queries/test-queries.ipynb +++ b/src/webapp/test_queries/test-queries.ipynb @@ -12,8 +12,8 @@ "execution_count": 1, "metadata": { "ExecuteTime": { - "end_time": "2024-01-30T16:27:44.277443Z", - "start_time": "2024-01-30T16:27:44.200678Z" + "end_time": "2024-02-29T13:59:09.647266Z", + "start_time": "2024-02-29T13:59:09.596489Z" } }, "outputs": [], @@ -33,8 +33,8 @@ "execution_count": 2, "metadata": { "ExecuteTime": { - "end_time": "2024-01-30T16:27:44.285218Z", - "start_time": "2024-01-30T16:27:44.279751Z" + "end_time": "2024-02-29T13:59:09.649352Z", + "start_time": "2024-02-29T13:59:09.644271Z" } }, "outputs": [], @@ -57,8 +57,8 @@ "execution_count": 3, "metadata": { "ExecuteTime": { - "end_time": "2024-01-30T16:27:45.832880Z", - "start_time": "2024-01-30T16:27:44.285324Z" + "end_time": "2024-02-29T13:59:12.865741Z", + "start_time": "2024-02-29T13:59:09.648952Z" } }, "outputs": [ @@ -85,14 +85,14 @@ "execution_count": 4, "metadata": { "ExecuteTime": { - "end_time": "2024-01-30T16:27:47.602756Z", - "start_time": "2024-01-30T16:27:45.830485Z" + "end_time": "2024-02-29T13:59:14.362831Z", + "start_time": "2024-02-29T13:59:12.866174Z" } }, "outputs": [ { "data": { - "text/plain": ")>" + "text/plain": ")>" }, "execution_count": 4, "metadata": {}, @@ -109,8 +109,8 @@ "execution_count": 5, "metadata": { "ExecuteTime": { - "end_time": "2024-01-30T16:27:49.203614Z", - "start_time": "2024-01-30T16:27:47.605358Z" + "end_time": "2024-02-29T13:59:17.313108Z", + "start_time": "2024-02-29T13:59:14.359360Z" } }, "outputs": [ @@ -145,8 +145,8 @@ "execution_count": 6, "metadata": { "ExecuteTime": { - "end_time": "2024-01-30T16:27:49.208774Z", - "start_time": "2024-01-30T16:27:49.201447Z" + "end_time": "2024-02-29T13:59:20.850223Z", + "start_time": "2024-02-29T13:59:20.827220Z" } }, "outputs": [ @@ -154,106 +154,106 @@ "name": "stdout", "output_type": "stream", "text": [ - "(http://edamontology.org/data_2646, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/format_3159, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", - "(http://edamontology.org/topic_0659, http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym, Functional RNA)\n", - "(http://edamontology.org/format_3015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/data_1193, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/format_2920, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.)\n", - "(http://edamontology.org/operation_2472, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/operation_0287, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", - "(http://edamontology.org/format_1915, http://www.w3.org/2004/02/skos/core#broadMatch, http://purl.org/dc/elements/1.1/format)\n", - "(http://edamontology.org/operation_0259, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/operations)\n", - "(http://edamontology.org/operation_0004, http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym, Lambda abstraction)\n", - "(http://edamontology.org/topic_3571, http://www.geneontology.org/formats/oboInOwl#hasDefinition, The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints.)\n", - "(http://edamontology.org/data_2770, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/data_2091)\n", - "(http://edamontology.org/data_2676, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division).)\n", - "(http://edamontology.org/topic_0121, http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym, MS-based untargeted proteomics)\n", - "(http://edamontology.org/format_3010, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/operation_2421, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/operations)\n", - "(http://edamontology.org/operation_3896, http://www.w3.org/2000/01/rdf-schema#seeAlso, https://en.wikipedia.org/wiki/Active_site)\n", - "(http://edamontology.org/topic_3060, http://www.w3.org/2002/07/owl#deprecated, true)\n", - "(http://edamontology.org/data_1015, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/identifiers)\n", - "(http://edamontology.org/topic_3574, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/format_3781, http://www.w3.org/2000/01/rdf-schema#label, PubAnnotation format)\n", - "(http://edamontology.org/data_3498, http://www.geneontology.org/formats/oboInOwl#hasExactSynonym, Gene sequence variations)\n", - "(http://edamontology.org/data_1014, http://edamontology.org/oldParent, http://www.w3.org/2002/07/owl#Thing)\n", - "(http://edamontology.org/data_2759, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/data_2091)\n", - "(http://edamontology.org/topic_2819, http://edamontology.org/deprecation_comment, (jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).)\n", - "(http://edamontology.org/operation_1831, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/operation_2442, http://www.w3.org/2000/01/rdf-schema#label, DNA structure prediction)\n", - "(http://edamontology.org/operation_0420, http://www.geneontology.org/formats/oboInOwl#hasExactSynonym, Protein-nucleic acid binding detection)\n", - "(http://edamontology.org/format_1475, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/formats)\n", - "(http://edamontology.org/data_1157, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/identifiers)\n", - "(http://edamontology.org/format_1935, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/format_3486)\n", - "(http://edamontology.org/operation_3227, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/operation_2478)\n", - "(http://edamontology.org/topic_0175, http://www.geneontology.org/formats/oboInOwl#consider, http://edamontology.org/topic_2275)\n", - "(http://edamontology.org/operation_3566, http://edamontology.org/created_in, 1.9)\n", - "(http://edamontology.org/topic_3535, http://www.w3.org/2000/01/rdf-schema#label, Protein-nucleic acid binding sites)\n", - "(http://edamontology.org/operation_0413, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/data_2704, http://www.geneontology.org/formats/oboInOwl#hasDefinition, A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).)\n", - "(http://edamontology.org/format_1455, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/formats)\n", - "(http://edamontology.org/data_1893, http://www.geneontology.org/formats/oboInOwl#hasDefinition, A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.)\n", - "(http://edamontology.org/operation_0519, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/obsolete)\n", - "(http://edamontology.org/operation_3964, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", - "(http://edamontology.org/data_1201, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/data_0847)\n", - "(http://edamontology.org/data_2907, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/data_2973, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Data concerning molecular secondary structure data.)\n", - "(http://edamontology.org/format_3699, http://www.w3.org/2000/01/rdf-schema#label, VDB)\n", - "(http://edamontology.org/data_2741, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/data_2091)\n", - "(http://edamontology.org/data_3134, http://www.w3.org/2000/01/rdf-schema#label, Gene transcript report)\n", - "(http://edamontology.org/operation_3218, http://www.geneontology.org/formats/oboInOwl#hasExactSynonym, Sequencing QC)\n", - "(http://edamontology.org/data_3722, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/topic_0787, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://www.w3.org/2002/07/owl#DeprecatedClass)\n", - "(http://edamontology.org/operation_0226, http://edamontology.org/notRecommendedForAnnotation, true)\n", - "(http://edamontology.org/operation_2410, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://www.w3.org/2002/07/owl#DeprecatedClass)\n", - "(http://edamontology.org/format_3910, http://www.w3.org/2000/01/rdf-schema#comment, The first 4 bytes of any trr file containing 1993. See https://github.com/galaxyproject/galaxy/pull/6597/files#diff-409951594551183dbf886e24de6cb129R760)\n", - "(http://edamontology.org/operation_1835, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/operation_0445, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", - "(Ne3435459b81443b682e791ffdbe6d0d7, http://www.w3.org/2002/07/owl#onProperty, http://edamontology.org/has_output)\n", - "(http://edamontology.org/format_1988, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/data_3716, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/data_1857, http://www.geneontology.org/formats/oboInOwl#hasDefinition, The fraction of an atom type present at a site in a molecular structure.)\n", - "(http://edamontology.org/format_3909, http://edamontology.org/ontology_used, http://edamontology.org/data_2301)\n", - "(http://edamontology.org/format_3098, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Format of raw SCOP domain classification data files.)\n", - "(http://edamontology.org/topic_2840, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Toxins and the adverse effects of these chemical substances on living organisms.)\n", - "(http://edamontology.org/data_2248, http://edamontology.org/oldParent, http://www.w3.org/2002/07/owl#Thing)\n", - "(http://edamontology.org/data_1407, http://edamontology.org/oldParent, http://www.w3.org/2002/07/owl#Thing)\n", - "(http://edamontology.org/data_3856, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/operation_0274, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://www.w3.org/2002/07/owl#DeprecatedClass)\n", - "(http://edamontology.org/data_2793, http://www.w3.org/2000/01/rdf-schema#label, SISYPHUS ID)\n", - "(http://edamontology.org/operation_0561, http://www.w3.org/2002/07/owl#deprecated, true)\n", - "(http://edamontology.org/topic_3408, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/events)\n", - "(http://edamontology.org/operation_3279, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Cluster (group) documents on the basis of their calculated similarity.)\n", - "(http://edamontology.org/data_2586, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/data_3424)\n", - "(http://edamontology.org/format_3876, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Trajectory Next Generation (TNG) is a format for storage of molecular simulation data. It is designed and implemented by the GROMACS development group, and it is called to be the substitute of the XTC format.)\n", - "(http://edamontology.org/operation_0226, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/topic_3050, http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId, Biodiversity)\n", - "(http://edamontology.org/operation_2426, http://www.w3.org/2000/01/rdf-schema#subClassOf, Nc5698417af7b45b68b9496c00bbe134b)\n", - "(http://edamontology.org/operation_3092, http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym, Sequence profile database search)\n", - "(http://edamontology.org/format_3602, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/format_2333)\n", - "(http://edamontology.org/operation_3233, http://www.w3.org/2000/01/rdf-schema#comment, Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).)\n", - "(http://edamontology.org/operation_2950, http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym, HET group detection)\n", - "(http://edamontology.org/operation_2934, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/data_1330, http://edamontology.org/obsolete_since, beta12orEarlier)\n", - "(http://edamontology.org/data_2152, http://edamontology.org/obsolete_since, 1.5)\n", - "(http://edamontology.org/operation_2499, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/operation_2426)\n", - "(http://edamontology.org/format_3692, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", - "(http://edamontology.org/operation_0359, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence.)\n", - "(http://edamontology.org/topic_2271, http://www.w3.org/2000/01/rdf-schema#label, Structure database search)\n", - "(http://edamontology.org/data_2687, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://www.w3.org/2002/07/owl#DeprecatedClass)\n", - "(N5efe31d4a85449cd98a19a903648ff2e, http://www.w3.org/1999/02/22-rdf-syntax-ns#rest, N32d35e625e214555abfc891c51e566f6)\n", - "(http://edamontology.org/format_3772, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/format_1919)\n", - "(http://edamontology.org/operation_0401, http://edamontology.org/obsolete_since, 1.12)\n", - "(http://edamontology.org/data_0941, http://www.w3.org/2002/07/owl#deprecated, true)\n", - "(http://edamontology.org/format_1337, http://www.w3.org/2000/01/rdf-schema#label, lhf)\n", - "(http://edamontology.org/data_1663, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", - "(http://edamontology.org/topic_2869, http://edamontology.org/created_in, beta12orEarlier)\n", - "(Nec1456a8ee3843be8b4dd4f3287977c1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Restriction)\n", - "(http://edamontology.org/data_2358, http://edamontology.org/created_in, beta12orEarlier)\n", - "(http://edamontology.org/topic_3420, http://www.w3.org/2000/01/rdf-schema#label, Reproductive health)\n", - "(http://edamontology.org/operation_3797, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/operations)\n", - "(http://edamontology.org/format_3626, http://edamontology.org/created_in, 1.12)\n" + "(http://edamontology.org/data_0874, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/data)\n", + "(http://edamontology.org/format_1980, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/topic_3415, http://edamontology.org/isdebtag, true)\n", + "(http://edamontology.org/operation_0004, http://www.w3.org/2002/07/owl#disjointWith, http://edamontology.org/topic_0003)\n", + "(http://edamontology.org/topic_2828, http://www.w3.org/2000/01/rdf-schema#label, X-ray diffraction)\n", + "(http://edamontology.org/operation_3431, http://www.geneontology.org/formats/oboInOwl#hasExactSynonym, Database submission)\n", + "(http://edamontology.org/format_2182, http://www.geneontology.org/formats/oboInOwl#hasDefinition, A text format resembling FASTQ short read format.)\n", + "(http://edamontology.org/data_1656, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/data_2198, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/topic_4020, http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym, Biogeochemical cycle)\n", + "(N93e90f33ebb749a486b5895d3f0446a8, http://www.w3.org/2002/07/owl#onProperty, http://edamontology.org/is_identifier_of)\n", + "(N2f3376d119664710a081491fdde147ac, http://www.w3.org/2002/07/owl#someValuesFrom, http://edamontology.org/data_0962)\n", + "(http://edamontology.org/topic_3541, http://edamontology.org/obsolete_since, 1.13)\n", + "(http://edamontology.org/data_2966, http://edamontology.org/created_in, beta12orEarlier)\n", + "(http://edamontology.org/operation_0402, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/operation_0337)\n", + "(N5a05d2a1e169418b82b9b5d52cd72f75, http://www.w3.org/2002/07/owl#someValuesFrom, http://edamontology.org/data_2048)\n", + "(http://edamontology.org/data_2365, http://www.geneontology.org/formats/oboInOwl#hasDefinition, A persistent, unique identifier of a biological pathway or network (typically a database entry).)\n", + "(http://edamontology.org/data_3111, http://edamontology.org/created_in, beta13)\n", + "(http://edamontology.org/data_2959, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://www.w3.org/2002/07/owl#DeprecatedClass)\n", + "(http://edamontology.org/operation_0317, http://edamontology.org/obsolete_since, beta12orEarlier)\n", + "(http://edamontology.org/format_1610, http://www.w3.org/2000/01/rdf-schema#label, KEGG GENES gene report format)\n", + "(http://edamontology.org/data_2220, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/identifiers)\n", + "(N4865fa91aa4a4909b84c55fbb68eaf6a, http://www.w3.org/2002/07/owl#onProperty, http://edamontology.org/has_input)\n", + "(http://edamontology.org/data_1560, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/data_2019, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/operation_3927, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", + "(http://edamontology.org/data_2385, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/identifiers)\n", + "(http://edamontology.org/operation_0312, http://www.w3.org/2000/01/rdf-schema#label, Sequencing-based expression profile data processing)\n", + "(http://edamontology.org/topic_0078, http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId, Proteins)\n", + "(http://edamontology.org/data_2090, http://www.w3.org/2002/07/owl#deprecated, true)\n", + "(http://edamontology.org/operation_3896, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/data_0845, http://www.w3.org/2000/01/rdf-schema#label, Molecular charge)\n", + "(http://edamontology.org/format_1551, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Format of output of the Pcons Model Quality Assessment Program (MQAP).)\n", + "(http://edamontology.org/data_1234, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", + "(http://edamontology.org/data_2902, http://edamontology.org/created_in, beta12orEarlier)\n", + "(http://edamontology.org/data_1007, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/data)\n", + "(http://edamontology.org/data_1567, http://edamontology.org/obsolete_since, 1.8)\n", + "(http://edamontology.org/data_2085, http://www.geneontology.org/formats/oboInOwl#hasExactSynonym, Structure-derived report)\n", + "(http://edamontology.org/format_4035, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/format_1475)\n", + "(http://edamontology.org/operation_0579, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/operation_0573)\n", + "(http://edamontology.org/data_2103, http://edamontology.org/obsolete_since, 1.3)\n", + "(http://edamontology.org/operation_2407, http://www.w3.org/2002/07/owl#deprecated, true)\n", + "(http://edamontology.org/data_1469, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/data_1368, http://www.geneontology.org/formats/oboInOwl#consider, http://edamontology.org/data_1354)\n", + "(http://edamontology.org/topic_2811, http://edamontology.org/obsolete_since, 1.3)\n", + "(http://edamontology.org/format_4039, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/format_2330)\n", + "(http://edamontology.org/format_3970, http://www.w3.org/2000/01/rdf-schema#label, Vega-lite)\n", + "(N2466636111704f33969af63f49b373fe, http://www.w3.org/2002/07/owl#someValuesFrom, http://edamontology.org/topic_0123)\n", + "(http://edamontology.org/operation_0525, http://www.w3.org/2000/01/rdf-schema#label, Genome assembly)\n", + "(http://edamontology.org/format_3825, http://edamontology.org/created_in, 1.20)\n", + "(http://edamontology.org/data_1597, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", + "(http://edamontology.org/format_3009, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/formats)\n", + "(http://edamontology.org/format_1197, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.)\n", + "(http://edamontology.org/format_3818, http://edamontology.org/documentation, http://ccg.vital-it.ch/chipseq/elandformat.php)\n", + "(http://edamontology.org/format_1606, http://edamontology.org/oldParent, http://www.w3.org/2002/07/owl#Thing)\n", + "(http://edamontology.org/data_2335, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/format_3556, http://www.w3.org/2000/01/rdf-schema#label, MHTML)\n", + "(N9ee8dc747e754712b3b1e4595251638d, http://www.w3.org/2002/07/owl#onProperty, http://edamontology.org/is_format_of)\n", + "(http://edamontology.org/data_2294, http://edamontology.org/created_in, beta12orEarlier)\n", + "(http://edamontology.org/data_1035, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/data_2091)\n", + "(http://edamontology.org/format_2919, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/formats)\n", + "(http://edamontology.org/operation_0253, http://www.geneontology.org/formats/oboInOwl#hasExactSynonym, Sequence feature prediction)\n", + "(http://edamontology.org/operation_0357, http://edamontology.org/oldParent, http://www.w3.org/2002/07/owl#Thing)\n", + "(http://edamontology.org/format_1969, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/bio)\n", + "(http://edamontology.org/operation_1818, http://www.geneontology.org/formats/oboInOwl#replacedBy, http://edamontology.org/operation_0387)\n", + "(http://edamontology.org/topic_0779, http://www.geneontology.org/formats/oboInOwl#hasDefinition, Mitochondria, typically of mitochondrial genes and proteins.)\n", + "(http://edamontology.org/operation_0342, http://edamontology.org/oldParent, http://www.w3.org/2002/07/owl#Thing)\n", + "(http://edamontology.org/operation_0295, http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym, 3D profile alignment)\n", + "(http://edamontology.org/operation_2507, http://edamontology.org/oldParent, http://edamontology.org/operation_2501)\n", + "(Nf2c8f98522d54c3cbe51cbf5c273c597, http://www.w3.org/2002/07/owl#annotatedTarget, http://www.w3.org/2000/01/rdf-schema#label)\n", + "(http://edamontology.org/operation_3088, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(N87dc94b8ec5e4282ad583cf4d85dc4d5, http://www.w3.org/2002/07/owl#someValuesFrom, http://edamontology.org/data_1461)\n", + "(http://edamontology.org/data_0884, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://www.w3.org/2002/07/owl#DeprecatedClass)\n", + "(http://edamontology.org/format_3327, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/format_2333)\n", + "(http://edamontology.org/format_3879, http://www.geneontology.org/formats/oboInOwl#hasExactSynonym, CG topology format)\n", + "(http://edamontology.org/operation_2404, http://www.w3.org/2000/01/rdf-schema#label, Sequence motif analysis)\n", + "(http://edamontology.org/data_0963, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/topic_3343, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/topics)\n", + "(http://edamontology.org/format_1651, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/operation_4033, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/operation_3664)\n", + "(http://edamontology.org/data_1592, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/operation_3929, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/operation_2423)\n", + "(http://edamontology.org/data_1069, http://edamontology.org/notRecommendedForAnnotation, true)\n", + "(http://edamontology.org/operation_2502, http://edamontology.org/oldParent, http://edamontology.org/operation_2945)\n", + "(http://edamontology.org/data_2354, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/data)\n", + "(http://edamontology.org/data_2615, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/data)\n", + "(http://edamontology.org/operation_3279, http://edamontology.org/created_in, 1.3)\n", + "(http://edamontology.org/format_3549, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/format_3547)\n", + "(http://edamontology.org/topic_0157, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/topics)\n", + "(http://edamontology.org/data_2318, http://www.w3.org/2000/01/rdf-schema#subClassOf, http://edamontology.org/data_2316)\n", + "(Nce0b14eb8c574a78a8ddeb7abc74ff0a, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Restriction)\n", + "(http://edamontology.org/data_1767, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/data_1726, http://www.w3.org/2002/07/owl#deprecated, true)\n", + "(http://edamontology.org/data_2674, http://www.w3.org/2000/01/rdf-schema#label, Ensembl ID ('Cavia porcellus'))\n", + "(http://edamontology.org/format_1950, http://www.w3.org/2000/01/rdf-schema#label, pdbatom)\n", + "(Nbb7120a9d7524db1b42250501a73b78e, http://www.w3.org/2002/07/owl#someValuesFrom, http://edamontology.org/data_1636)\n", + "(http://edamontology.org/data_1157, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class)\n", + "(http://edamontology.org/format_1614, http://www.w3.org/2002/07/owl#deprecated, true)\n", + "(http://edamontology.org/data_1143, http://www.geneontology.org/formats/oboInOwl#inSubset, http://edamontology.org/identifiers)\n", + "(http://edamontology.org/format_3248, http://www.geneontology.org/formats/oboInOwl#hasDefinition, mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics.)\n" ] } ], @@ -274,8 +274,8 @@ "execution_count": 7, "metadata": { "ExecuteTime": { - "end_time": "2024-01-30T16:27:49.247949Z", - "start_time": "2024-01-30T16:27:49.209354Z" + "end_time": "2024-02-29T13:59:23.067118Z", + "start_time": "2024-02-29T13:59:23.059459Z" } }, "outputs": [], @@ -336,8 +336,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-30T16:27:49.372889Z", - "start_time": "2024-01-30T16:27:49.226457Z" + "end_time": "2024-02-29T13:59:26.200878Z", + "start_time": "2024-02-29T13:59:26.082715Z" } }, "execution_count": 8 @@ -349,20 +349,20 @@ "name": "stdout", "output_type": "stream", "text": [ - "Topic 'Literature and language' has no 'seeAlso' property.\n", - "Topic 'Data submission, annotation, and curation' has no 'seeAlso' property.\n", - "Topic 'Data identity and mapping' has no 'seeAlso' property.\n", - "Topic 'Genome resequencing' has no 'seeAlso' property.\n", - "Topic 'Simulation experiment' has no 'seeAlso' property.\n", - "Topic 'Nucleic acid sites, features and motifs' has no 'seeAlso' property.\n", - "Topic 'Protein properties' has no 'seeAlso' property.\n", - "Topic 'Protein sites, features and motifs' has no 'seeAlso' property.\n", - "Topic 'Sequence composition, complexity and repeats' has no 'seeAlso' property.\n", - "Topic 'Probes and primers' has no 'seeAlso' property.\n", - "Topic 'Sequence sites, features and motifs' has no 'seeAlso' property.\n", - "Topic 'Biomolecular simulation' has no 'seeAlso' property.\n", - "Topic 'Biotherapeutics' has no 'seeAlso' property.\n", - "Topic 'Quality affairs' has no 'seeAlso' property.\n" + "Topic 'Literature and language' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Data submission, annotation, and curation' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Data identity and mapping' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Genome resequencing' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Simulation experiment' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Nucleic acid sites, features and motifs' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Protein properties' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Protein sites, features and motifs' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Sequence composition, complexity and repeats' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Probes and primers' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Sequence sites, features and motifs' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Biomolecular simulation' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Biotherapeutics' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Quality affairs' has no wikipedia link ('seeAlso' property).\n" ] } ], @@ -381,20 +381,1161 @@ " } .\n", "}\n", "\"\"\"\n", + "results = kg.query(query)\n", + "\n", + "\n", + "for r in results :\n", + " print(f\"Topic '{r['term']}' has no wikipedia link ('seeAlso' property).\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-29T14:07:01.337516Z", + "start_time": "2024-02-29T14:07:01.331591Z" + } + }, + "execution_count": 10 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "14\n", + "Topic 'Literature and language' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Data submission, annotation, and curation' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Data identity and mapping' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Genome resequencing' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Simulation experiment' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Nucleic acid sites, features and motifs' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Protein properties' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Protein sites, features and motifs' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Sequence composition, complexity and repeats' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Probes and primers' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Sequence sites, features and motifs' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Biomolecular simulation' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Biotherapeutics' has no wikipedia link ('seeAlso' property).\n", + "Topic 'Quality affairs' has no wikipedia link ('seeAlso' property).\n" + ] + } + ], + "source": [ + "import os\n", + "\n", + "query = os.path.dirname(\".\") + \"../queries/no_wikipedia_link_topic.rq\"\n", + "\n", + "with open(query, \"r\") as f:\n", + " query = f.read()\n", + " \n", + " results = kg.query(query)\n", + " nb_err = len(results)\n", + "f.close()\n", + "\n", + "print(nb_err)\n", + "\n", + "for r in results :\n", + " print(f\"Topic '{r['term']}' has no wikipedia link ('seeAlso' property).\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-29T14:18:57.077411Z", + "start_time": "2024-02-29T14:18:57.012981Z" + } + }, + "execution_count": 15 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query = os.path.dirname(\".\") + \"../queries/no_wikipedia_link_topic.rq\"\n", + "\n", + "with open(query, \"r\") as f:\n", + " query = f.read()\n", + " \n", + " results = kg.query(query)\n", + " nb_err = len(results)\n", + "f.close()\n", + "\n", + "print(nb_err)\n", + "\n", + "for r in results :\n", + " print(f\"Topic '{r['term']}' has no wikipedia link ('seeAlso' property).\") " + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Topic 'Informatics' has no broad synonym\n", + "Topic 'Ontology and terminology' has no broad synonym\n", + "Topic 'Bioinformatics' has no broad synonym\n", + "Topic 'Laboratory information management' has no broad synonym\n", + "Topic 'Cheminformatics' has no broad synonym\n", + "Topic 'Chemometrics' has no broad synonym\n", + "Topic 'Medical informatics' has no broad synonym\n", + "Topic 'Immunoinformatics' has no broad synonym\n", + "Topic 'Literature and language' has no broad synonym\n", + "Topic 'Natural language processing' has no broad synonym\n", + "Topic 'Data management' has no broad synonym\n", + "Topic 'Data submission, annotation, and curation' has no broad synonym\n", + "Topic 'Workflows' has no broad synonym\n", + "Topic 'Data acquisition' has no broad synonym\n", + "Topic 'Data security' has no broad synonym\n", + "Topic 'Data identity and mapping' has no broad synonym\n", + "Topic 'Data architecture, analysis and design' has no broad synonym\n", + "Topic 'Data integration and warehousing' has no broad synonym\n", + "Topic 'Data governance' has no broad synonym\n", + "Topic 'Data quality management' has no broad synonym\n", + "Topic 'Data rescue' has no broad synonym\n", + "Topic 'FAIR data' has no broad synonym\n", + "Topic 'Biochemistry' has no broad synonym\n", + "Topic 'Microfluidics' has no broad synonym\n", + "Topic 'Computational chemistry' has no broad synonym\n", + "Topic 'Drug discovery' has no broad synonym\n", + "Topic 'Medicinal chemistry' has no broad synonym\n", + "Topic 'Compound libraries and screening' has no broad synonym\n", + "Topic 'Analytical chemistry' has no broad synonym\n", + "Topic 'Synthetic chemistry' has no broad synonym\n", + "Topic 'Chemical biology' has no broad synonym\n", + "Topic 'Mathematics' has no broad synonym\n", + "Topic 'Statistics and probability' has no broad synonym\n", + "Topic 'Applied mathematics' has no broad synonym\n", + "Topic 'Pure mathematics' has no broad synonym\n", + "Topic 'Computer science' has no broad synonym\n", + "Topic 'Software engineering' has no broad synonym\n", + "Topic 'Physics' has no broad synonym\n", + "Topic 'Biophysics' has no broad synonym\n", + "Topic 'Acoustics' has no broad synonym\n", + "Topic 'Laboratory techniques' has no broad synonym\n", + "Topic 'Sequencing' has no broad synonym\n", + "Topic 'ChIP-seq' has no broad synonym\n", + "Topic 'RNA-Seq' has no broad synonym\n", + "Topic 'Whole genome sequencing' has no broad synonym\n", + "Topic 'Exome sequencing' has no broad synonym\n", + "Topic 'Metagenomic sequencing' has no broad synonym\n", + "Topic 'Single-Cell Sequencing' has no broad synonym\n", + "Topic 'Imaging' has no broad synonym\n", + "Topic 'Cryogenic electron microscopy' has no broad synonym\n", + "Topic 'X-ray diffraction' has no broad synonym\n", + "Topic 'Bioimaging' has no broad synonym\n", + "Topic 'Medical imaging' has no broad synonym\n", + "Topic 'Light microscopy' has no broad synonym\n", + "Topic 'MRI' has no broad synonym\n", + "Topic 'Neutron diffraction' has no broad synonym\n", + "Topic 'Tomography' has no broad synonym\n", + "Topic 'Echography' has no broad synonym\n", + "Topic 'Electroencephalography' has no broad synonym\n", + "Topic 'Electrocardiography' has no broad synonym\n", + "Topic 'Genotyping experiment' has no broad synonym\n", + "Topic 'Microarray experiment' has no broad synonym\n", + "Topic 'PCR experiment' has no broad synonym\n", + "Topic 'Proteomics experiment' has no broad synonym\n", + "Topic 'RNAi experiment' has no broad synonym\n", + "Topic 'Simulation experiment' has no broad synonym\n", + "Topic 'Immunoprecipitation experiment' has no broad synonym\n", + "Topic 'ChIP-on-chip' has no broad synonym\n", + "Topic 'Methylated DNA immunoprecipitation' has no broad synonym\n", + "Topic 'RNA immunoprecipitation' has no broad synonym\n", + "Topic 'Cytometry' has no broad synonym\n", + "Topic 'Chromosome conformation capture' has no broad synonym\n", + "Topic 'Protein interaction experiment' has no broad synonym\n", + "Topic 'Experimental design and studies' has no broad synonym\n", + "Topic 'Preclinical and clinical studies' has no broad synonym\n", + "Topic 'GWAS study' has no broad synonym\n", + "Topic 'Animal study' has no broad synonym\n", + "Topic 'Environmental sciences' has no broad synonym\n", + "Topic 'Ecology' has no broad synonym\n", + "Topic 'Biodiversity' has no broad synonym\n", + "Topic 'Microbial ecology' has no broad synonym\n", + "Topic 'Metabarcoding' has no broad synonym\n", + "Topic 'Open science' has no broad synonym\n", + "Topic 'Biosciences' has no broad synonym\n", + "Topic 'Biology' has no broad synonym\n", + "Topic 'Model organisms' has no broad synonym\n", + "Topic 'Plant biology' has no broad synonym\n", + "Topic 'Virology' has no broad synonym\n", + "Topic 'Structural biology' has no broad synonym\n", + "Topic 'Structural genomics' has no broad synonym\n", + "Topic 'Cell biology' has no broad synonym\n", + "Topic 'Systems biology' has no broad synonym\n", + "Topic 'Human biology' has no broad synonym\n", + "Topic 'Molecular biology' has no broad synonym\n", + "Topic 'Genetics' has no broad synonym\n", + "Topic 'Genotype and phenotype' has no broad synonym\n", + "Topic 'Quantitative genetics' has no broad synonym\n", + "Topic 'Phenomics' has no broad synonym\n", + "Topic 'Molecular evolution' has no broad synonym\n", + "Topic 'Epistasis' has no broad synonym\n", + "Topic 'Population genetics' has no broad synonym\n", + "Topic 'Epigenetics' has no broad synonym\n", + "Topic 'Epigenomics' has no broad synonym\n", + "Topic 'Genomic imprinting' has no broad synonym\n", + "Topic 'Molecular genetics' has no broad synonym\n", + "Topic 'Gene structure' has no broad synonym\n", + "Topic 'Functional, regulatory and non-coding RNA' has no broad synonym\n", + "Topic 'Mobile genetic elements' has no broad synonym\n", + "Topic 'Gene transcripts' has no broad synonym\n", + "Topic 'Genetic variation' has no broad synonym\n", + "Topic 'DNA mutation' has no broad synonym\n", + "Topic 'DNA polymorphism' has no broad synonym\n", + "Topic 'Structural variation' has no broad synonym\n", + "Topic 'Copy number variation' has no broad synonym\n", + "Topic 'Gene expression' has no broad synonym\n", + "Topic 'Gene regulation' has no broad synonym\n", + "Topic 'Transcription factors and regulatory sites' has no broad synonym\n", + "Topic 'Transcriptomics' has no broad synonym\n", + "Topic 'Metatranscriptomics' has no broad synonym\n", + "Topic 'Ribosome Profiling' has no broad synonym\n", + "Topic 'RNA splicing' has no broad synonym\n", + "Topic 'Gene and protein families' has no broad synonym\n", + "Topic 'Immunoproteins and antigens' has no broad synonym\n", + "Topic 'Cytogenetics' has no broad synonym\n", + "Topic 'Human genetics' has no broad synonym\n", + "Topic 'Genetic engineering' has no broad synonym\n", + "Topic 'Immunogenetics' has no broad synonym\n", + "Topic 'Developmental biology' has no broad synonym\n", + "Topic 'Embryology' has no broad synonym\n", + "Topic 'Biotechnology' has no broad synonym\n", + "Topic 'Biomaterials' has no broad synonym\n", + "Topic 'Bioengineering' has no broad synonym\n", + "Topic 'Medical biotechnology' has no broad synonym\n", + "Topic 'Synthetic biology' has no broad synonym\n", + "Topic 'Metabolic engineering' has no broad synonym\n", + "Topic 'Evolutionary biology' has no broad synonym\n", + "Topic 'Phylogeny' has no broad synonym\n", + "Topic 'Phylogenetics' has no broad synonym\n", + "Topic 'Cladistics' has no broad synonym\n", + "Topic 'Taxonomy' has no broad synonym\n", + "Topic 'Microbiology' has no broad synonym\n", + "Topic 'Antimicrobial Resistance' has no broad synonym\n", + "Topic 'Biomarkers' has no broad synonym\n", + "Topic 'Marine biology' has no broad synonym\n", + "Topic 'Zoology' has no broad synonym\n", + "Topic 'Medicine' has no broad synonym\n", + "Topic 'Pathology' has no broad synonym\n", + "Topic 'Infectious disease' has no broad synonym\n", + "Topic 'Rare diseases' has no broad synonym\n", + "Topic 'Oncology' has no broad synonym\n", + "Topic 'Toxicology' has no broad synonym\n", + "Topic 'Physiology' has no broad synonym\n", + "Topic 'Public health and epidemiology' has no broad synonym\n", + "Topic 'Respiratory medicine' has no broad synonym\n", + "Topic 'Neurology' has no broad synonym\n", + "Topic 'Cardiology' has no broad synonym\n", + "Topic 'Translational medicine' has no broad synonym\n", + "Topic 'Molecular medicine' has no broad synonym\n", + "Topic 'Systems medicine' has no broad synonym\n", + "Topic 'Veterinary medicine' has no broad synonym\n", + "Topic 'Allergy, clinical immunology and immunotherapeutics' has no broad synonym\n", + "Topic 'Pain medicine' has no broad synonym\n", + "Topic 'Anaesthesiology' has no broad synonym\n", + "Topic 'Critical care medicine' has no broad synonym\n", + "Topic 'Dermatology' has no broad synonym\n", + "Topic 'Dentistry' has no broad synonym\n", + "Topic 'Ear, nose and throat medicine' has no broad synonym\n", + "Topic 'Endocrinology and metabolism' has no broad synonym\n", + "Topic 'Haematology' has no broad synonym\n", + "Topic 'Gastroenterology' has no broad synonym\n", + "Topic 'Gender medicine' has no broad synonym\n", + "Topic 'Gynaecology and obstetrics' has no broad synonym\n", + "Topic 'Hepatic and biliary medicine' has no broad synonym\n", + "Topic 'Trauma medicine' has no broad synonym\n", + "Topic 'Medical toxicology' has no broad synonym\n", + "Topic 'Musculoskeletal medicine' has no broad synonym\n", + "Topic 'Paediatrics' has no broad synonym\n", + "Topic 'Reproductive health' has no broad synonym\n", + "Topic 'Surgery' has no broad synonym\n", + "Topic 'Urology and nephrology' has no broad synonym\n", + "Topic 'Tropical medicine' has no broad synonym\n", + "Topic 'Personalised medicine' has no broad synonym\n", + "Topic 'Computational biology' has no broad synonym\n", + "Topic 'Nucleic acids' has no broad synonym\n", + "Topic 'Nucleic acid structure analysis' has no broad synonym\n", + "Topic 'RNA' has no broad synonym\n", + "Topic 'DNA' has no broad synonym\n", + "Topic 'DNA binding sites' has no broad synonym\n", + "Topic 'DNA replication and recombination' has no broad synonym\n", + "Topic 'DNA packaging' has no broad synonym\n", + "Topic 'Nucleic acid sites, features and motifs' has no broad synonym\n", + "Topic 'Proteins' has no broad synonym\n", + "Topic 'Protein expression' has no broad synonym\n", + "Topic 'Protein targeting and localisation' has no broad synonym\n", + "Topic 'Protein modifications' has no broad synonym\n", + "Topic 'Protein variants' has no broad synonym\n", + "Topic 'Protein properties' has no broad synonym\n", + "Topic 'Protein interactions' has no broad synonym\n", + "Topic 'Membrane and lipoproteins' has no broad synonym\n", + "Topic 'Enzymes' has no broad synonym\n", + "Topic 'Protein structure analysis' has no broad synonym\n", + "Topic 'Protein folding, stability and design' has no broad synonym\n", + "Topic 'Protein structural motifs and surfaces' has no broad synonym\n", + "Topic 'Protein folds and structural domains' has no broad synonym\n", + "Topic 'Protein disordered structure' has no broad synonym\n", + "Topic 'Protein secondary structure' has no broad synonym\n", + "Topic 'Protein sites, features and motifs' has no broad synonym\n", + "Topic 'Protein binding sites' has no broad synonym\n", + "Topic 'Sequence analysis' has no broad synonym\n", + "Topic 'Mapping' has no broad synonym\n", + "Topic 'Sequence composition, complexity and repeats' has no broad synonym\n", + "Topic 'Phylogenomics' has no broad synonym\n", + "Topic 'Sequence assembly' has no broad synonym\n", + "Topic 'Probes and primers' has no broad synonym\n", + "Topic 'Structure analysis' has no broad synonym\n", + "Topic 'Structure prediction' has no broad synonym\n", + "Topic 'Molecular modelling' has no broad synonym\n", + "Topic 'Carbohydrates' has no broad synonym\n", + "Topic 'Lipids' has no broad synonym\n", + "Topic 'Small molecules' has no broad synonym\n", + "Topic 'Sequence sites, features and motifs' has no broad synonym\n", + "Topic 'Molecular interactions, pathways and networks' has no broad synonym\n", + "Topic 'Function analysis' has no broad synonym\n", + "Topic 'Functional genomics' has no broad synonym\n", + "Topic 'Biomolecular simulation' has no broad synonym\n", + "Topic 'Biomedical science' has no broad synonym\n", + "Topic 'Pharmacology' has no broad synonym\n", + "Topic 'Pharmacogenomics' has no broad synonym\n", + "Topic 'Immunology' has no broad synonym\n", + "Topic 'Anatomy' has no broad synonym\n", + "Topic 'Sample collections' has no broad synonym\n", + "Topic 'Biobank' has no broad synonym\n", + "Topic 'Mouse clinic' has no broad synonym\n", + "Topic 'Microbial collection' has no broad synonym\n", + "Topic 'Cell culture collection' has no broad synonym\n", + "Topic 'Clone library' has no broad synonym\n", + "Topic 'Parasitology' has no broad synonym\n", + "Topic 'Drug development' has no broad synonym\n", + "Topic 'Drug metabolism' has no broad synonym\n", + "Topic 'Safety sciences' has no broad synonym\n", + "Topic 'Pharmacovigilance' has no broad synonym\n", + "Topic 'Quality affairs' has no broad synonym\n", + "Topic 'Regulatory affairs' has no broad synonym\n", + "Topic 'Vaccinology' has no broad synonym\n", + "Topic 'Laboratory animal science' has no broad synonym\n", + "Topic 'Nutritional science' has no broad synonym\n", + "Topic 'Regenerative medicine' has no broad synonym\n", + "Topic 'Omics' has no broad synonym\n", + "Topic 'Proteomics' has no broad synonym\n", + "Topic 'Genomics' has no broad synonym\n", + "Topic 'Comparative genomics' has no broad synonym\n", + "Topic 'Population genomics' has no broad synonym\n", + "Topic 'Proteogenomics' has no broad synonym\n", + "Topic 'Paleogenomics' has no broad synonym\n", + "Topic 'Metabolomics' has no broad synonym\n", + "Topic 'Fluxomics' has no broad synonym\n", + "Topic 'Immunomics' has no broad synonym\n", + "Topic 'Multiomics' has no broad synonym\n" + ] + } + ], + "source": [ + "## Query for synonyms\n", + "query = \"\"\"\n", + "PREFIX edam: \n", + "PREFIX oboInOwl: \n", + "\n", + "\n", + "SELECT ?term ?c WHERE {\n", + " ?c rdfs:subClassOf+ edam:topic_0003 ;\n", + " rdfs:label ?term .\n", + " FILTER NOT EXISTS {\n", + " ?c oboInOwl:hasBroadSynonym ?hasBroadSynonym .\n", + " } .\n", + "}\n", + "\"\"\"\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Topic '{r['term']}' has no broad synonym\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-29T15:17:02.172242Z", + "start_time": "2024-02-29T15:17:02.118429Z" + } + }, + "execution_count": 18 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "## Query for topics with no definition (ERROR level)\n", + "query = \"\"\"\n", + "PREFIX edam: \n", + "PREFIX oboInOwl: \n", + "\n", + "SELECT ?term ?concept WHERE {\n", + " ?concept rdfs:subClassOf+ edam:topic_0003 ;\n", + " rdfs:label ?term .\n", + " \n", + " FILTER NOT EXISTS {\n", + " ?concept oboInOwl:hasDefinition ?def \n", + " } .\n", + "}\n", + "\"\"\"\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Topic '{r['term']}' and '{r['concept']}' has no def \") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-29T15:38:16.752372Z", + "start_time": "2024-02-29T15:38:16.700550Z" + } + }, + "execution_count": 38 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Data term 'Textual format' has def 'Textual format.' \n", + "Data term 'SMILES' has def 'Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.' \n", + "Data term 'smarts' has def 'SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation.' \n", + "Data term 'InChI' has def 'Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.' \n", + "Data term 'mf' has def 'Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.' \n", + "Data term 'InChIKey' has def 'The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound.' \n", + "Data term 'nucleotide' has def 'Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.' \n", + "Data term 'pure nucleotide' has def 'Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters.' \n", + "Data term 'pure dna' has def 'Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters.' \n", + "Data term 'pure rna' has def 'Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters.' \n", + "Data term 'unambiguous pure nucleotide' has def 'Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters .' \n", + "Data term 'dna' has def 'Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters.' \n", + "Data term 'unambiguous pure dna' has def 'Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters.' \n", + "Data term 'completely unambiguous pure dna' has def 'Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters.' \n", + "Data term 'rna' has def 'Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters.' \n", + "Data term 'unambiguous pure rna sequence' has def 'Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters.' \n", + "Data term 'completely unambiguous pure rna sequence' has def 'Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters.' \n", + "Data term 'completely unambiguous pure nucleotide' has def 'Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters .' \n", + "Data term 'protein' has def 'Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.' \n", + "Data term 'unambiguous pure protein' has def 'Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters.' \n", + "Data term 'pure protein' has def 'Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.' \n", + "Data term 'completely unambiguous pure protein' has def 'Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters.' \n", + "Data term 'EMBL feature location' has def 'Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.' \n", + "Data term 'quicktandem' has def 'Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program).' \n", + "Data term 'Sanger inverted repeats' has def 'Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).' \n", + "Data term 'EMBOSS repeat' has def 'Report format for tandem repeats in a sequence (an EMBOSS report format).' \n", + "Data term 'est2genome format' has def 'Format of a report on exon-intron structure generated by EMBOSS est2genome.' \n", + "Data term 'restrict format' has def 'Report format for restriction enzyme recognition sites used by EMBOSS restrict program.' \n", + "Data term 'restover format' has def 'Report format for restriction enzyme recognition sites used by EMBOSS restover program.' \n", + "Data term 'REBASE restriction sites' has def 'Report format for restriction enzyme recognition sites used by REBASE database.' \n", + "Data term 'FASTA search results format' has def 'Format of results of a sequence database search using FASTA.' \n", + "Data term 'BLAST results' has def 'Format of results of a sequence database search using some variant of BLAST.' \n", + "Data term 'BLAST XML results format' has def 'XML format as produced by the NCBI Blast package.' \n", + "Data term 'BLAST XML v2 results format' has def 'XML format as produced by the NCBI Blast package v2.' \n", + "Data term 'mspcrunch' has def 'Format of results of a sequence database search using some variant of MSPCrunch.' \n", + "Data term 'Smith-Waterman format' has def 'Format of results of a sequence database search using some variant of Smith Waterman.' \n", + "Data term 'dhf' has def 'Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.' \n", + "Data term 'lhf' has def 'Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.' \n", + "Data term 'InterPro hits format' has def 'Results format for searches of the InterPro database.' \n", + "Data term 'InterPro protein view report format' has def 'Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.' \n", + "Data term 'InterPro match table format' has def 'Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.' \n", + "Data term 'HMMER Dirichlet prior' has def 'Dirichlet distribution HMMER format.' \n", + "Data term 'MEME Dirichlet prior' has def 'Dirichlet distribution MEME format.' \n", + "Data term 'HMMER emission and transition' has def 'Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model.' \n", + "Data term 'prosite-pattern' has def 'Format of a regular expression pattern from the Prosite database.' \n", + "Data term 'EMBOSS sequence pattern' has def 'Format of an EMBOSS sequence pattern.' \n", + "Data term 'meme-motif' has def 'A motif in the format generated by the MEME program.' \n", + "Data term 'prosite-profile' has def 'Sequence profile (sequence classifier) format used in the PROSITE database.' \n", + "Data term 'JASPAR format' has def 'A profile (sequence classifier) in the format used in the JASPAR database.' \n", + "Data term 'MEME background Markov model' has def 'Format of the model of random sequences used by MEME.' \n", + "Data term 'HMMER format' has def 'Format of a hidden Markov model representation used by the HMMER package.' \n", + "Data term 'HMMER2' has def 'HMMER profile HMM file for HMMER versions 2.x.' \n", + "Data term 'HMMER3' has def 'HMMER profile HMM file for HMMER versions 3.x.' \n", + "Data term 'HMMER-aln' has def 'FASTA-style format for multiple sequences aligned by HMMER package to an HMM.' \n", + "Data term 'DIALIGN format' has def 'Format of multiple sequences aligned by DIALIGN package.' \n", + "Data term 'daf' has def 'EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family.' \n", + "Data term 'Sequence-MEME profile alignment' has def 'Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.' \n", + "Data term 'HMMER profile alignment (sequences versus HMMs)' has def 'Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.' \n", + "Data term 'HMMER profile alignment (HMM versus sequences)' has def 'Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database.' \n", + "Data term 'Phylip distance matrix' has def 'Format of PHYLIP phylogenetic distance matrix data.' \n", + "Data term 'ClustalW dendrogram' has def 'Dendrogram (tree file) format generated by ClustalW.' \n", + "Data term 'Phylip tree raw' has def 'Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted.' \n", + "Data term 'Phylip continuous quantitative characters' has def 'PHYLIP file format for continuous quantitative character data.' \n", + "Data term 'Phylip character frequencies format' has def 'PHYLIP file format for phylogenetics character frequency data.' \n", + "Data term 'Phylip discrete states format' has def 'Format of PHYLIP discrete states data.' \n", + "Data term 'Phylip cliques format' has def 'Format of PHYLIP cliques data.' \n", + "Data term 'Phylip tree format' has def 'Phylogenetic tree data format used by the PHYLIP program.' \n", + "Data term 'TreeBASE format' has def 'The format of an entry from the TreeBASE database of phylogenetic data.' \n", + "Data term 'TreeFam format' has def 'The format of an entry from the TreeFam database of phylogenetic data.' \n", + "Data term 'Phylip tree distance format' has def 'Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package.' \n", + "Data term 'dssp' has def 'Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).' \n", + "Data term 'hssp' has def 'Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins).' \n", + "Data term 'Dot-bracket format' has def 'Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server.' \n", + "Data term 'Vienna local RNA secondary structure format' has def 'Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server.' \n", + "Data term 'PDB' has def 'Entry format of PDB database in PDB format.' \n", + "Data term 'mmCIF' has def 'Entry format of PDB database in mmCIF format.' \n", + "Data term 'aaindex' has def 'Amino acid index format used by the AAindex database.' \n", + "Data term 'Pcons report format' has def 'Format of output of the Pcons Model Quality Assessment Program (MQAP).' \n", + "Data term 'ProQ report format' has def 'Format of output of the ProQ protein model quality predictor.' \n", + "Data term 'findkm' has def 'A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax).' \n", + "Data term 'Primer3 primer' has def 'Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program.' \n", + "Data term 'mira' has def 'Format of MIRA sequence trace information file.' \n", + "Data term 'CAF' has def 'Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.' \n", + "Data term 'EXP' has def 'Sequence assembly project file EXP format.' \n", + "Data term 'PHD' has def 'PHD sequence trace format to store serialised chromatogram data (reads).' \n", + "Data term 'dat' has def 'Format of Affymetrix data file of raw image data.' \n", + "Data term 'cel' has def 'Format of Affymetrix data file of information about (raw) expression levels of the individual probes.' \n", + "Data term 'affymetrix' has def 'Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering.' \n", + "Data term 'affymetrix-exp' has def 'Affymetrix data file format for information about experimental conditions and protocols.' \n", + "Data term 'CHP' has def 'Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.' \n", + "Data term 'HET group dictionary entry format' has def 'The format of an entry from the HET group dictionary (HET groups from PDB files).' \n", + "Data term 'PubMed citation' has def 'Format of bibliographic reference as used by the PubMed database.' \n", + "Data term 'Medline Display Format' has def 'Format for abstracts of scientific articles from the Medline database.' \n", + "Data term 'CiteXplore-core' has def 'CiteXplore 'core' citation format including title, journal, authors and abstract.' \n", + "Data term 'CiteXplore-all' has def 'CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references.' \n", + "Data term 'pmc' has def 'Article format of the PubMed Central database.' \n", + "Data term 'OSCAR format' has def 'OSCAR format of annotated chemical text.' \n", + "Data term 'PlasMapper TextMap' has def 'Map of a plasmid (circular DNA) in PlasMapper TextMap format.' \n", + "Data term 'newick' has def 'Phylogenetic tree Newick (text) format.' \n", + "Data term 'TreeCon format' has def 'Phylogenetic tree TreeCon (text) format.' \n", + "Data term 'Nexus format' has def 'Phylogenetic tree Nexus (text) format.' \n", + "Data term 'acedb' has def 'ACEDB sequence format.' \n", + "Data term 'codata' has def 'Codata entry format.' \n", + "Data term 'Staden experiment format' has def 'Staden experiment file format.' \n", + "Data term 'fitch program' has def 'Fitch program format.' \n", + "Data term 'GCG' has def 'GCG sequence file format.' \n", + "Data term 'hennig86' has def 'Hennig86 output sequence format.' \n", + "Data term 'ig' has def 'Intelligenetics sequence format.' \n", + "Data term 'igstrict' has def 'Intelligenetics sequence format (strict version).' \n", + "Data term 'jackknifer' has def 'Jackknifer interleaved and non-interleaved sequence format.' \n", + "Data term 'mase format' has def 'Mase program sequence format.' \n", + "Data term 'mega-seq' has def 'Mega interleaved and non-interleaved sequence format.' \n", + "Data term 'nbrf/pir' has def 'NBRF/PIR entry sequence format.' \n", + "Data term 'nexus-seq' has def 'Nexus/paup interleaved sequence format.' \n", + "Data term 'pdbatom' has def 'PDB sequence format (ATOM lines).' \n", + "Data term 'pdbatomnuc' has def 'PDB nucleotide sequence format (ATOM lines).' \n", + "Data term 'pdbseqresnuc' has def 'PDB nucleotide sequence format (SEQRES lines).' \n", + "Data term 'pdbseqres' has def 'PDB sequence format (SEQRES lines).' \n", + "Data term 'raw' has def 'Raw sequence format with no non-sequence characters.' \n", + "Data term 'refseqp' has def 'Refseq protein entry sequence format.' \n", + "Data term 'Staden format' has def 'Staden suite sequence format.' \n", + "Data term 'Stockholm format' has def 'Stockholm multiple sequence alignment format (used by Pfam and Rfam).' \n", + "Data term 'strider format' has def 'DNA strider output sequence format.' \n", + "Data term 'plain text format (unformatted)' has def 'Plain text sequence format (essentially unformatted).' \n", + "Data term 'ASN.1 sequence format' has def 'NCBI ASN.1-based sequence format.' \n", + "Data term 'debug-seq' has def 'EMBOSS debugging trace sequence format of full internal data content.' \n", + "Data term 'jackknifernon' has def 'Jackknifer output sequence non-interleaved format.' \n", + "Data term 'nexusnon' has def 'Nexus/paup non-interleaved sequence format.' \n", + "Data term 'debug-feat' has def 'EMBOSS debugging trace feature format of full internal data content.' \n", + "Data term 'ClustalW format' has def 'ClustalW format for (aligned) sequences.' \n", + "Data term 'debug' has def 'EMBOSS alignment format for debugging trace of full internal data content.' \n", + "Data term 'match' has def 'Alignment format for start and end of matches between sequence pairs.' \n", + "Data term 'scores format' has def 'Alignment format for score values for pairs of sequences.' \n", + "Data term 'selex' has def 'SELEX format for (aligned) sequences.' \n", + "Data term 'EMBOSS simple format' has def 'EMBOSS simple multiple alignment format.' \n", + "Data term 'srs format' has def 'Simple multiple sequence (alignment) format for SRS.' \n", + "Data term 'srspair' has def 'Simple sequence pair (alignment) format for SRS.' \n", + "Data term 'T-Coffee format' has def 'T-Coffee program alignment format.' \n", + "Data term 'TreeCon-seq' has def 'Treecon format for (aligned) sequences.' \n", + "Data term 'pure' has def 'Alphabet for molecular sequence with possible unknown positions but without non-sequence characters.' \n", + "Data term 'unambiguous pure' has def 'Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters.' \n", + "Data term 'completely unambiguous pure' has def 'Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters.' \n", + "Data term 'unpure' has def 'Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters.' \n", + "Data term 'consensus' has def 'Alphabet for the consensus of two or more molecular sequences.' \n", + "Data term 'unambiguous sequence' has def 'Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters.' \n", + "Data term 'ambiguous' has def 'Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters.' \n", + "Data term 'EMBL-like (text)' has def 'A text format resembling EMBL entry format.' \n", + "Data term 'EMBL format' has def 'EMBL entry format.' \n", + "Data term 'geneseq' has def 'Geneseq sequence format.' \n", + "Data term 'FASTQ-like format (text)' has def 'A text format resembling FASTQ short read format.' \n", + "Data term 'FASTQ' has def 'FASTQ short read format ignoring quality scores.' \n", + "Data term 'FASTQ-illumina' has def 'FASTQ Illumina 1.3 short read format.' \n", + "Data term 'qualillumina' has def 'FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8.' \n", + "Data term 'FASTQ-sanger' has def 'FASTQ short read format with phred quality.' \n", + "Data term 'FASTQ-solexa' has def 'FASTQ Solexa/Illumina 1.0 short read format.' \n", + "Data term 'qualsolexa' has def 'FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format.' \n", + "Data term 'qual' has def 'FASTQ format subset for Phred sequencing quality score data only (no sequences).' \n", + "Data term 'qualsolid' has def 'FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data.' \n", + "Data term 'qual454' has def 'FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers.' \n", + "Data term 'UniProt-like (text)' has def 'A text sequence format resembling uniprotkb entry format.' \n", + "Data term 'UniProtKB format' has def 'UniProtKB entry sequence format.' \n", + "Data term 'medline' has def 'Abstract format used by MedLine database.' \n", + "Data term 'FASTA-like (text)' has def 'A text format resembling FASTA format.' \n", + "Data term 'dbid' has def 'Fasta format variant with database name before ID.' \n", + "Data term 'FASTA' has def 'FASTA format including NCBI-style IDs.' \n", + "Data term 'giFASTA format' has def 'FASTA sequence format including NCBI-style GIs.' \n", + "Data term 'Pearson format' has def 'Plain old FASTA sequence format (unspecified format for IDs).' \n", + "Data term 'NCBI format' has def 'NCBI FASTA sequence format with NCBI-style IDs.' \n", + "Data term 'FASTA-aln' has def 'Fasta format for (aligned) sequences.' \n", + "Data term 'A2M' has def 'The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA.' \n", + "Data term 'csfasta' has def 'Color space FASTA format sequence variant.' \n", + "Data term 'XMFA' has def 'XMFA format stands for eXtended Multi-FastA format and is used to store collinear sub-alignments that constitute a single genome alignment.' \n", + "Data term 'GenBank-like format (text)' has def 'A text format resembling GenBank entry (plain text) format.' \n", + "Data term 'GenBank format' has def 'Genbank entry format.' \n", + "Data term 'genpept' has def 'Genpept protein entry format.' \n", + "Data term 'GFF' has def 'GFF feature format (of indeterminate version).' \n", + "Data term 'GFF2' has def 'General Feature Format (GFF) of sequence features.' \n", + "Data term 'GFF2-seq' has def 'GFF feature file format with sequence in the header.' \n", + "Data term 'GFF3' has def 'Generic Feature Format version 3 (GFF3) of sequence features.' \n", + "Data term 'GFF3-seq' has def 'GFF3 feature file format with sequence.' \n", + "Data term 'GVF' has def 'Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation.' \n", + "Data term 'mirGFF3' has def 'mirGFF3 is a common format for microRNA data resulting from small-RNA RNA-Seq workflows.' \n", + "Data term 'GTF' has def 'Gene Transfer Format (GTF), a restricted version of GFF.' \n", + "Data term 'OBO' has def 'OBO ontology text format.' \n", + "Data term 'completely unambiguous' has def 'Alphabet for a molecular sequence without any unknown positions or ambiguity characters.' \n", + "Data term 'SAM' has def 'Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.' \n", + "Data term 'markx0 variant' has def 'Some variant of Pearson MARKX alignment format.' \n", + "Data term 'markx0' has def 'Pearson MARKX0 alignment format.' \n", + "Data term 'markx1' has def 'Pearson MARKX1 alignment format.' \n", + "Data term 'markx10' has def 'Pearson MARKX10 alignment format.' \n", + "Data term 'markx2' has def 'Pearson MARKX2 alignment format.' \n", + "Data term 'markx3' has def 'Pearson MARKX3 alignment format.' \n", + "Data term 'mega variant' has def 'Some variant of Mega format for (typically aligned) sequences.' \n", + "Data term 'mega' has def 'Mega format for (typically aligned) sequences.' \n", + "Data term 'meganon' has def 'Mega non-interleaved format for (typically aligned) sequences.' \n", + "Data term 'Phylip format variant' has def 'Some variant of Phylip format for (aligned) sequences.' \n", + "Data term 'PHYLIP format' has def 'Phylip format for (aligned) sequences.' \n", + "Data term 'PHYLIP sequential' has def 'Phylip non-interleaved format for (aligned) sequences.' \n", + "Data term 'Relaxed PHYLIP Interleaved' has def 'Phylip multiple alignment sequence format, less stringent than PHYLIP format.' \n", + "Data term 'Relaxed PHYLIP Sequential' has def 'Phylip multiple alignment sequence format, less stringent than PHYLIP sequential format (format_1998).' \n", + "Data term 'ACE' has def 'ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).' \n", + "Data term 'BED' has def 'Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.' \n", + "Data term 'bedstrict' has def 'Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns.' \n", + "Data term 'bed6' has def 'BED file format where each feature is described by chromosome, start, end, name, score, and strand.' \n", + "Data term 'ENCODE peak format' has def 'Human ENCODE peak format.' \n", + "Data term 'ENCODE narrow peak format' has def 'Human ENCODE narrow peak format.' \n", + "Data term 'ENCODE broad peak format' has def 'Human ENCODE broad peak format.' \n", + "Data term 'bed12' has def 'A BED file where each feature is described by all twelve columns.' \n", + "Data term 'chrominfo' has def 'Tabular format of chromosome names and sizes used by Galaxy.' \n", + "Data term 'WIG' has def 'Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser.' \n", + "Data term 'PSL' has def 'PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.' \n", + "Data term 'MAF' has def 'Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.' \n", + "Data term 'genePred' has def 'genePred table format for gene prediction tracks.' \n", + "Data term 'pgSnp' has def 'Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.' \n", + "Data term 'axt' has def 'axt format of alignments, typically produced from BLASTZ.' \n", + "Data term 'LAV' has def 'LAV format of alignments generated by BLASTZ and LASTZ.' \n", + "Data term 'Pileup' has def 'Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s).' \n", + "Data term 'VCF' has def 'Variant Call Format (VCF) is tabular format for storing genomic sequence variations.' \n", + "Data term 'gVCF' has def 'Genomic Variant Call Format (gVCF) is a version of VCF that includes not only the positions that are variant when compared to a reference genome, but also the non-variant positions as ranges, including metrics of confidence that the positions in the range are actually non-variant e.g. minimum read-depth and genotype quality.' \n", + "Data term 'GTrack' has def 'GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation (\"machine understandability\").' \n", + "Data term 'Cytoband format' has def 'Cytoband format for chromosome cytobands.' \n", + "Data term 'PSI MI TAB (MITAB)' has def 'Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI.' \n", + "Data term 'OWL Functional Syntax' has def 'A human-readable encoding for the Web Ontology Language (OWL).' \n", + "Data term 'Manchester OWL Syntax' has def 'A syntax for writing OWL class expressions.' \n", + "Data term 'KRSS2 Syntax' has def 'A superset of the \"Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort\".' \n", + "Data term 'Turtle' has def 'The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs.' \n", + "Data term 'N-Triples' has def 'A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.' \n", + "Data term 'Notation3' has def 'A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind.' \n", + "Data term 'PED/MAP' has def 'The PED/MAP file describes data used by the Plink package.' \n", + "Data term 'MAP' has def 'The MAP file describes SNPs and is used by the Plink package.' \n", + "Data term 'PED' has def 'The PED file describes individuals and genetic data and is used by the Plink package.' \n", + "Data term 'CT' has def 'File format of a CT (Connectivity Table) file from the RNAstructure package.' \n", + "Data term 'SS' has def 'XRNA old input style format.' \n", + "Data term 'GDE' has def 'Format for the Genetic Data Environment (GDE).' \n", + "Data term 'Cytoscape input file format' has def 'Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments.' \n", + "Data term 'GCG format variant' has def 'Some format based on the GCG format.' \n", + "Data term 'GCG MSF' has def 'GCG MSF (multiple sequence file) file format.' \n", + "Data term 'RSF' has def 'Rich sequence format.' \n", + "Data term 'Ensembl variation file format' has def 'Ensembl standard format for variation data.' \n", + "Data term 'mhd' has def 'Text-based tagged file format for medical images generated using the MetaImage software package.' \n", + "Data term 'nrrd' has def 'Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data.' \n", + "Data term 'R file format' has def 'File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics.' \n", + "Data term 'SPSS' has def 'File format used for scripts for the Statistical Package for the Social Sciences.' \n", + "Data term 'rcc' has def 'Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts.' \n", + "Data term 'arff' has def 'ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes.' \n", + "Data term 'afg' has def 'AFG is a single text-based file assembly format that holds read and consensus information together.' \n", + "Data term 'bedgraph' has def 'The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data.' \n", + "Data term 'customtrack' has def 'Custom Sequence annotation track format used by Galaxy.' \n", + "Data term 'mzTab' has def 'mzTab is a tab-delimited format for mass spectrometry-based proteomics and metabolomics results.' \n", + "Data term 'ISA-TAB' has def 'The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates metadata from experiments employing a combination of technologies.' \n", + "Data term 'SBtab' has def 'SBtab is a tabular format for biochemical network models.' \n", + "Data term 'BEL' has def 'Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form.' \n", + "Data term 'AGP' has def 'AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome).' \n", + "Data term 'PS' has def 'PostScript format.' \n", + "Data term 'EPS' has def 'Encapsulated PostScript format.' \n", + "Data term 'GCT/Res format' has def 'Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample.' \n", + "Data term 'Mascot .dat file' has def '\"Raw\" result file from Mascot database search.' \n", + "Data term 'MaxQuant APL peaklist format' has def 'Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra.' \n", + "Data term 'LocARNA PP' has def 'The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record.' \n", + "Data term 'dbGaP format' has def 'Input format used by the Database of Genotypes and Phenotypes (dbGaP).' \n", + "Data term 'BIOM format' has def 'The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables.' \n", + "Data term 'DSV' has def 'Tabular data represented as values in a text file delimited by some character.' \n", + "Data term 'TSV' has def 'Tabular data represented as tab-separated values in a text file.' \n", + "Data term 'MAGE-TAB' has def 'MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED).' \n", + "Data term 'WEGO' has def 'WEGO native format used by the Web Gene Ontology Annotation Plot application. Tab-delimited format with gene names and others GO IDs (columns) with one annotation record per line.' \n", + "Data term 'RPKM' has def 'Tab-delimited format for gene expression levels table, calculated as Reads Per Kilobase per Million (RPKM) mapped reads.' \n", + "Data term 'PEtab' has def 'A data format for specifying parameter estimation problems in systems biology.' \n", + "Data term 'CSV' has def 'Tabular data represented as comma-separated values in a text file.' \n", + "Data term 'SEQUEST .out file' has def '\"Raw\" result file from SEQUEST database search.' \n", + "Data term 'GSuite' has def 'GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata.' \n", + "Data term 'MCPD' has def 'The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information.' \n", + "Data term 'PubTator format' has def 'Native textual export format of annotated scientific text from PubTator.' \n", + "Data term 'BioNLP Shared Task format' has def 'A family of similar formats of text annotation, used by BRAT and other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format, BRAT standoff format, and similar.' \n", + "Data term 'SQL' has def 'SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases.' \n", + "Data term 'XQuery' has def 'XQuery (XML Query) is a query language (format of queries) for querying and manipulating structured and unstructured data, usually in the form of XML, text, and with vendor-specific extensions for other data formats (JSON, binary, etc.).' \n", + "Data term 'SPARQL' has def 'SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format.' \n", + "Data term 'GEN' has def 'The GEN file format contains genetic data and describes SNPs.' \n", + "Data term 'SAMPLE file format' has def 'The SAMPLE file format contains information about each individual i.e. individual IDs, covariates, phenotypes and missing data proportions, from a GWAS study.' \n", + "Data term 'SDF' has def 'SDF is one of a family of chemical-data file formats developed by MDL Information Systems; it is intended especially for structural information.' \n", + "Data term 'Molfile' has def 'An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule.' \n", + "Data term 'Mol2' has def 'Complete, portable representation of a SYBYL molecule. ASCII file which contains all the information needed to reconstruct a SYBYL molecule.' \n", + "Data term 'latex' has def 'format for the LaTeX document preparation system.' \n", + "Data term 'ELAND format' has def 'Tab-delimited text file format used by Eland - the read-mapping program distributed by Illumina with its sequencing analysis pipeline - which maps short Solexa sequence reads to the human reference genome.' \n", + "Data term 'GML' has def 'GML (Graph Modeling Language) is a text file format supporting network data with a very easy syntax. It is used by Graphlet, Pajek, yEd, LEDA and NetworkX.' \n", + "Data term 'FASTG' has def 'FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty.' \n", + "Data term 'proBED' has def '. proBED is an adaptation of BED (format_3003), which was extended to meet specific requirements entailed by proteomics data.' \n", + "Data term 'GPR' has def 'GenePix Results (GPR) text file format developed by Axon Instruments that is used to save GenePix Results data.' \n", + "Data term 'JCAMP-DX' has def 'A standardized file format for data exchange in mass spectrometry, initially developed for infrared spectrometry.' \n", + "Data term 'XYZ' has def 'The XYZ chemical file format is widely supported by many programs, although many slightly different XYZ file formats coexist (Tinker XYZ, UniChem XYZ, etc.). Basic information stored for each atom in the system are x, y and z coordinates and atom element/atomic number.' \n", + "Data term 'mdcrd' has def 'AMBER trajectory (also called mdcrd), with 10 coordinates per line and format F8.3 (fixed point notation with field width 8 and 3 decimal places).' \n", + "Data term 'GROMACS top' has def 'GROMACS MD package top textual files define an entire structure system topology, either directly, or by including itp files.' \n", + "Data term 'AMBER top' has def 'AMBER Prmtop file (version 7) is a structure topology text file divided in several sections designed to be parsed easily using simple Fortran code. Each section contains particular topology information, such as atom name, charge, mass, angles, dihedrals, etc.' \n", + "Data term 'PSF' has def 'X-Plor Protein Structure Files (PSF) are structure topology files used by NAMD and CHARMM molecular simulations programs. PSF files contain six main sections of interest: atoms, bonds, angles, dihedrals, improper dihedrals (force terms used to maintain planarity) and cross-terms.' \n", + "Data term 'GROMACS itp' has def 'GROMACS itp files (include topology) contain structure topology information, and are typically included in GROMACS topology files (GROMACS top). Itp files are used to define individual (or multiple) components of a topology as a separate file. This is particularly useful if there is a molecule that is used frequently, and also reduces the size of the system topology file, splitting it in different parts.' \n", + "Data term 'RST' has def 'AMBER coordinate/restart file with 6 coordinates per line and decimal format F12.7 (fixed point notation with field width 12 and 7 decimal places).' \n", + "Data term 'CHARMM rtf' has def 'Format of CHARMM Residue Topology Files (RTF), which define groups by including the atoms, the properties of the group, and bond and charge information.' \n", + "Data term 'AMBER frcmod' has def 'AMBER frcmod (Force field Modification) is a file format to store any modification to the standard force field needed for a particular molecule to be properly represented in the simulation.' \n", + "Data term 'AMBER off' has def 'AMBER Object File Format library files (OFF library files) store residue libraries (forcefield residue parameters).' \n", + "Data term 'NMReDATA' has def 'MReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or \"NMReDATA\") includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc.' \n", + "Data term 'BpForms' has def 'BpForms is a string format for concretely representing the primary structures of biopolymers, including DNA, RNA, and proteins that include non-canonical nucleic and amino acids. See https://www.bpforms.org for more information.' \n", + "Data term 'trr' has def 'Format of trr files that contain the trajectory of a simulation experiment used by GROMACS.' \n", + "Data term 'MTX' has def 'The Matrix Market matrix (MTX) format stores numerical or pattern matrices in a dense (array format) or sparse (coordinate format) representation.' \n", + "Data term 'BcForms' has def 'BcForms is a format for abstractly describing the molecular structure (atoms and bonds) of macromolecular complexes as a collection of subunits and crosslinks. Each subunit can be described with BpForms (http://edamontology.org/format_3909) or SMILES (http://edamontology.org/data_2301). BcForms uses an ontology of crosslinks to abstract the chemical details of crosslinks from the descriptions of complexes (see https://bpforms.org/crosslink.html).' \n", + "Data term 'N-Quads' has def 'N-Quads is a line-based, plain text format for encoding an RDF dataset. It includes information about the graph each triple belongs to.' \n", + "Data term 'BNGL' has def 'BioNetGen is a format for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks.' \n", + "Data term 'GFA 1' has def 'Graphical Fragment Assembly captures sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology.' \n", + "Data term 'GFA 2' has def 'Graphical Fragment Assembly captures sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology. GFA2 is an update of GFA1 which is not compatible with GFA1.' \n", + "Data term 'CONTIG' has def 'The CONTIG format used for output of the SOAPdenovo alignment program. It contains contig sequences generated without using mate pair information.' \n", + "Data term 'CHAIN' has def 'The CHAIN format describes a pairwise alignment that allow gaps in both sequences simultaneously and is used by the UCSC Genome Browser.' \n", + "Data term 'NET' has def 'The NET file format is used to describe the data that underlie the net alignment annotations in the UCSC Genome Browser.' \n", + "Data term 'QMAP' has def 'Format of QMAP files generated for methylation data from an internal BGI pipeline.' \n", + "Data term 'gxformat2' has def 'An emerging format for high-level Galaxy workflow description.' \n", + "Data term 'CIGAR format' has def 'Compact Idiosyncratic Gapped Alignment Report format is a compressed (run-length encoded) pairwise alignment format. It is useful for representing long (e.g. genomic) pairwise alignments.' \n", + "Data term 'Python script' has def 'Format for scripts writtenin Python - a widely used high-level programming language for general-purpose programming.' \n", + "Data term 'Perl script' has def 'Format for scripts written in Perl - a family of high-level, general-purpose, interpreted, dynamic programming languages.' \n", + "Data term 'R script' has def 'Format for scripts written in the R language - an open source programming language and software environment for statistical computing and graphics that is supported by the R Foundation for Statistical Computing.' \n", + "Data term 'R markdown' has def 'A file format for making dynamic documents (R Markdown scripts) with the R language.' \n", + "Data term 'Configuration file format' has def 'A configuration file used by various programs to store settings that are specific to their respective software.' \n", + "Data term 'MATLAB script' has def 'The file format for MATLAB scripts or functions.' \n", + "Data term 'BioSimulators standard for command-line interfaces for biosimulation tools' has def 'Outlines the syntax and semantics of the input and output arguments for command-line interfaces for biosimulation tools.' \n", + "Data term 'PQR' has def 'Data format derived from the standard PDB format, which enables user to incorporate parameters for charge and radius to the existing PDB data file.' \n", + "Data term 'PDBQT' has def 'Data format used in AutoDock 4 for storing atomic coordinates, partial atomic charges and AutoDock atom types for both receptors and ligands.' \n", + "Data term 'MSP' has def 'MSP is a data format for mass spectrometry data.' \n", + "Data term 'HTML' has def 'HTML format.' \n", + "Data term 'iHOP format' has def 'The format of iHOP (Information Hyperlinked over Proteins) text-mining result.' \n", + "Data term 'FASTA-HTML' has def 'FASTA format wrapped in HTML elements.' \n", + "Data term 'EMBL-HTML' has def 'EMBL entry format wrapped in HTML elements.' \n", + "Data term 'GenBank-HTML' has def 'Genbank entry format wrapped in HTML elements.' \n", + "Data term 'MHTML' has def 'MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on.' \n", + "Data term 'XML' has def 'eXtensible Markup Language (XML) format.' \n", + "Data term 'PDBML' has def 'Entry format of PDB database in PDBML (XML) format.' \n", + "Data term 'Taverna workflow format' has def 'Format of Taverna workflows.' \n", + "Data term 'DAS format' has def 'DAS sequence (XML) format (any type).' \n", + "Data term 'dasdna' has def 'DAS sequence (XML) format (nucleotide-only).' \n", + "Data term 'DASGFF' has def 'DAS GFF (XML) feature format.' \n", + "Data term 'STRING entry format (XML)' has def 'Entry format (XML) for the STRING database of protein interaction.' \n", + "Data term 'BioXSD (XML)' has def 'BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming.' \n", + "Data term 'OBO-XML' has def 'OBO ontology XML format.' \n", + "Data term 'EMBL-like (XML)' has def 'An XML format resembling EMBL entry format.' \n", + "Data term 'EMBL format (XML)' has def 'An XML format for EMBL entries.' \n", + "Data term 'EMBLXML' has def 'XML format for EMBL entries.' \n", + "Data term 'cdsxml' has def 'Specific XML format for EMBL entries (only uses certain sections).' \n", + "Data term 'INSDSeq' has def 'INSDSeq provides the elements of a sequence as presented in the GenBank/EMBL/DDBJ-style flatfile formats, with a small amount of additional structure.' \n", + "Data term 'SBML' has def 'Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.' \n", + "Data term 'SBRML' has def 'Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models.' \n", + "Data term 'EBI Application Result XML' has def 'EBI Application Result XML is a format returned by sequence similarity search Web services at EBI.' \n", + "Data term 'PSI MI XML (MIF)' has def 'XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI.' \n", + "Data term 'PSI-PAR' has def 'Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema.' \n", + "Data term 'phyloXML' has def 'phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data.' \n", + "Data term 'NeXML' has def 'NeXML is a standardised XML format for rich phyloinformatic data.' \n", + "Data term 'MAGE-ML' has def 'MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED).' \n", + "Data term 'GCDML' has def 'GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC).' \n", + "Data term 'CopasiML' has def 'CopasiML, the native format of COPASI.' \n", + "Data term 'CellML' has def 'CellML, the format for mathematical models of biological and other networks.' \n", + "Data term 'mzML' has def 'mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.' \n", + "Data term 'TraML' has def 'TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS.' \n", + "Data term 'mzIdentML' has def 'mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines.' \n", + "Data term 'mzQuantML' has def 'mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics.' \n", + "Data term 'GelML' has def 'GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS.' \n", + "Data term 'spML' has def 'spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics.' \n", + "Data term 'RDF/XML' has def 'Resource Description Framework (RDF) XML format.' \n", + "Data term 'OWL/XML' has def 'OWL ontology XML serialisation format.' \n", + "Data term 'RNAML' has def 'RNA Markup Language.' \n", + "Data term 'xls' has def 'Microsoft Excel spreadsheet format.' \n", + "Data term 'BSML' has def 'Bioinformatics Sequence Markup Language format.' \n", + "Data term 'docx' has def 'Microsoft Word format.' \n", + "Data term 'SVG' has def 'Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation.' \n", + "Data term 'pepXML' has def 'Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses.' \n", + "Data term 'GPML' has def 'Graphical Pathway Markup Language (GPML) is an XML format used for exchanging biological pathways.' \n", + "Data term 'imzML metadata file' has def 'imzML metadata is a data format for mass spectrometry imaging metadata.' \n", + "Data term 'qcML' has def 'qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements.' \n", + "Data term 'PRIDE XML' has def 'PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment.' \n", + "Data term 'SED-ML' has def 'Simulation Experiment Description Markup Language (SED-ML) is an XML format for encoding simulation setups, according to the MIASE (Minimum Information About a Simulation Experiment) requirements.' \n", + "Data term 'BCML' has def 'Biological Connection Markup Language (BCML) is an XML format for biological pathways.' \n", + "Data term 'BDML' has def 'Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics.' \n", + "Data term 'SBGN-ML' has def 'SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks.' \n", + "Data term 'X!Tandem XML' has def 'Output format used by X! series search engines that is based on the XML language BIOML.' \n", + "Data term 'SBOL' has def 'Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology.' \n", + "Data term 'PMML' has def 'PMML uses XML to represent mining models. The structure of the models is described by an XML Schema.' \n", + "Data term 'protXML' has def 'A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data.' \n", + "Data term 'idXML' has def 'XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS.' \n", + "Data term 'UniProtKB XML' has def 'UniProtKB XML sequence features format is an XML format available for downloading UniProt entries.' \n", + "Data term 'BioC' has def 'BioC is a standardised XML format for sharing and integrating text data and annotations.' \n", + "Data term 'xsd' has def 'XML format for XML Schema.' \n", + "Data term 'VisML' has def 'Default XML format of VisANT, containing all the network information.' \n", + "Data term 'nmrML' has def 'nmrML is an MSI supported XML-based open access format for metabolomics NMR raw and processed spectral data. It is accompanies by an nmrCV (controlled vocabulary) to allow ontology-based annotations.' \n", + "Data term 'consensusXML' has def 'OpenMS format for grouping features in one map or across several maps.' \n", + "Data term 'featureXML' has def 'OpenMS format for quantitation results (LC/MS features).' \n", + "Data term 'mzData' has def 'Now deprecated data format of the HUPO Proteomics Standards Initiative. Replaced by mzML (format_3244).' \n", + "Data term 'TIDE TXT' has def 'Format supported by the Tide tool for identifying peptides from tandem mass spectra.' \n", + "Data term 'pptx' has def 'Microsoft Powerpoint format.' \n", + "Data term 'BEAST' has def 'XML input file format for BEAST Software (Bayesian Evolutionary Analysis Sampling Trees).' \n", + "Data term 'Chado-XML' has def 'Chado-XML format is a direct mapping of the Chado relational schema into XML.' \n", + "Data term 'HSAML' has def 'An alignment format generated by PRANK/PRANKSTER consisting of four elements: newick, nodes, selection and model.' \n", + "Data term 'InterProScan XML' has def 'Output xml file from the InterProScan sequence analysis application.' \n", + "Data term 'KGML' has def 'The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format.' \n", + "Data term 'PubMed XML' has def 'XML format for collected entries from bibliographic databases MEDLINE and PubMed.' \n", + "Data term 'OrthoXML' has def 'OrthoXML is designed broadly to allow the storage and comparison of orthology data from any ortholog database. It establishes a structure for describing orthology relationships while still allowing flexibility for database-specific information to be encapsulated in the same format.' \n", + "Data term 'PSDML' has def 'Tree structure of Protein Sequence Database Markup Language generated using Matra software.' \n", + "Data term 'SeqXML' has def 'SeqXML is an XML Schema to describe biological sequences, developed by the Stockholm Bioinformatics Centre.' \n", + "Data term 'UniParc XML' has def 'XML format for the UniParc database.' \n", + "Data term 'UniRef XML' has def 'XML format for the UniRef reference clusters.' \n", + "Data term 'NeuroML' has def 'A model description language for computational neuroscience.' \n", + "Data term 'cml' has def 'Chemical Markup Language (CML) is an XML-based format for encoding detailed information about a wide range of chemical concepts.' \n", + "Data term 'Binary format' has def 'Binary format.' \n", + "Data term 'ABI' has def 'A format of raw sequence read data from an Applied Biosystems sequencing machine.' \n", + "Data term 'SCF' has def 'Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata.' \n", + "Data term 'BAM' has def 'BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.' \n", + "Data term 'AB1' has def 'AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence.' \n", + "Data term 'bigBed' has def 'bigBed format for large sequence annotation tracks, similar to textual BED format.' \n", + "Data term 'bigWig' has def 'bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.' \n", + "Data term '2bit' has def '2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'.' \n", + "Data term '.nib' has def '.nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'.' \n", + "Data term 'SRF' has def 'Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.' \n", + "Data term 'ZTR' has def 'ZTR format for storing chromatogram data from DNA sequencing instruments.' \n", + "Data term 'BCF' has def 'BCF is the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).' \n", + "Data term 'SFF' has def 'Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing.' \n", + "Data term 'BAI' has def 'BAM indexing format.' \n", + "Data term 'CRAM' has def 'Reference-based compression of alignment format.' \n", + "Data term 'GIF' has def 'Graphics Interchange Format.' \n", + "Data term 'ebwt' has def 'Bowtie format for indexed reference genome for \"small\" genomes.' \n", + "Data term 'ebwtl' has def 'Bowtie format for indexed reference genome for \"large\" genomes.' \n", + "Data term 'PDF' has def 'Portable Document Format.' \n", + "Data term 'DICOM format' has def 'Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.' \n", + "Data term 'nii' has def 'An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI) commonly used to store brain imaging data obtained using Magnetic Resonance Imaging (MRI) methods.' \n", + "Data term 'IDAT' has def 'Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array.' \n", + "Data term 'JPG' has def 'Joint Picture Group file format for lossy graphics file.' \n", + "Data term 'HDF5' has def 'HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF).' \n", + "Data term 'Loom' has def 'The Loom file format is based on HDF5, a standard for storing large numerical datasets. The Loom format is designed to efficiently hold large omics datasets. Typically, such data takes the form of a large matrix of numbers, along with metadata for the rows and columns.' \n", + "Data term 'TIFF' has def 'A versatile bitmap format.' \n", + "Data term 'BMP' has def 'Standard bitmap storage format in the Microsoft Windows environment.' \n", + "Data term 'im' has def 'IM is a format used by LabEye and other applications based on the IFUNC image processing library.' \n", + "Data term 'pcd' has def 'Photo CD format, which is the highest resolution format for images on a CD.' \n", + "Data term 'pcx' has def 'PCX is an image file format that uses a simple form of run-length encoding. It is lossless.' \n", + "Data term 'ppm' has def 'The PPM format is a lowest common denominator color image file format.' \n", + "Data term 'psd' has def 'PSD (Photoshop Document) is a proprietary file that allows the user to work with the images' individual layers even after the file has been saved.' \n", + "Data term 'xbm' has def 'X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI.' \n", + "Data term 'xpm' has def 'X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels.' \n", + "Data term 'rgb' has def 'RGB file format is the native raster graphics file format for Silicon Graphics workstations.' \n", + "Data term 'pbm' has def 'The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters.' \n", + "Data term 'pgm' has def 'The PGM format is a lowest common denominator grayscale file format.' \n", + "Data term 'PNG' has def 'PNG is a file format for image compression.' \n", + "Data term 'rast' has def 'Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems.' \n", + "Data term 'bgzip' has def 'Blocked GNU Zip format.' \n", + "Data term 'tabix' has def 'TAB-delimited genome position file index format.' \n", + "Data term 'xlsx' has def 'MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file.' \n", + "Data term 'ObjTables' has def 'ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of classes). ObjTables consists of a format for describing schemas for spreadsheets, numerous data types for science, a syntax for indicating the class and attribute represented by each table and column in a workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets.' \n", + "Data term 'SQLite format' has def 'Data format used by the SQLite database.' \n", + "Data term 'Gemini SQLite format' has def 'Data format used by the SQLite database conformant to the Gemini schema.' \n", + "Data term 'snpeffdb' has def 'An index of a genome database, indexed for use by the snpeff tool.' \n", + "Data term 'netCDF' has def 'Format used by netCDF software library for writing and reading chromatography-MS data files. Also used to store trajectory atom coordinates information, such as the ones obtained by Molecular Dynamics simulations.' \n", + "Data term 'K-mer countgraph' has def 'A list of k-mers and their occurrences in a dataset. Can also be used as an implicit De Bruijn graph.' \n", + "Data term 'COMBINE OMEX' has def 'Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology.' \n", + "Data term 'SRA format' has def 'SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive.' \n", + "Data term 'VDB' has def 'VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive.' \n", + "Data term 'Tabix index file format' has def 'Index file format used by the samtools package to index TAB-delimited genome position files.' \n", + "Data term 'WIFF format' has def 'Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex).' \n", + "Data term 'Thermo RAW' has def 'Proprietary file format for mass spectrometry data from Thermo Scientific.' \n", + "Data term 'OME-TIFF' has def 'Image file format used by the Open Microscopy Environment (OME).' \n", + "Data term 'BTrack' has def 'BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats.' \n", + "Data term 'proBAM' has def '. proBAM is an adaptation of BAM (format_2572), which was extended to meet specific requirements entailed by proteomics data.' \n", + "Data term 'ARB' has def 'Binary format used by the ARB software suite.' \n", + "Data term 'ibd' has def 'ibd is a data format for mass spectrometry imaging data.' \n", + "Data term 'MSAML' has def 'A set of XML compliant markup components for describing multiple sequence alignments.' \n", + "Data term 'Waters RAW' has def 'Proprietary file format for mass spectrometry data from Waters.' \n", + "Data term 'HDF' has def 'HDF is the name of a set of file formats and libraries designed to store and organize large amounts of numerical data, originally developed at the National Center for Supercomputing Applications at the University of Illinois.' \n", + "Data term 'PCAzip' has def 'PCAZip format is a binary compressed file to store atom coordinates based on Essential Dynamics (ED) and Principal Component Analysis (PCA).' \n", + "Data term 'XTC' has def 'Portable binary format for trajectories produced by GROMACS package.' \n", + "Data term 'TNG' has def 'Trajectory Next Generation (TNG) is a format for storage of molecular simulation data. It is designed and implemented by the GROMACS development group, and it is called to be the substitute of the XTC format.' \n", + "Data term 'BinPos' has def 'Scripps Research Institute BinPos format is a binary formatted file to store atom coordinates.' \n", + "Data term 'msh' has def 'Mash sketch is a format for sequence / sequence checksum information. To make a sketch, each k-mer in a sequence is hashed, which creates a pseudo-random identifier. By sorting these hashes, a small subset from the top of the sorted list can represent the entire sequence.' \n", + "Data term 'Zarr' has def 'The Zarr format is an implementation of chunked, compressed, N-dimensional arrays for storing data.' \n", + "Data term 'Docker image' has def 'A Docker image is a file, comprised of multiple layers, that is used to execute code in a Docker container. An image is essentially built from the instructions for a complete and executable version of an application, which relies on the host OS kernel.' \n", + "Data term 'TAR format' has def 'TAR archive file format generated by the Unix-based utility tar.' \n", + "Data term 'WMV' has def 'The proprietary native video format of various Microsoft programs such as Windows Media Player.' \n", + "Data term 'ZIP format' has def 'ZIP is an archive file format that supports lossless data compression.' \n", + "Data term 'LSM' has def 'Zeiss' proprietary image format based on TIFF.' \n", + "Data term 'GZIP format' has def 'GNU zip compressed file format common to Unix-based operating systems.' \n", + "Data term 'AVI' has def 'Audio Video Interleaved (AVI) format is a multimedia container format for AVI files, that allows synchronous audio-with-video playback.' \n", + "Data term 'TrackDB' has def 'A declaration file format for UCSC browsers track dataset display charateristics.' \n", + "Data term 'Stereolithography format' has def 'STL is a file format native to the stereolithography CAD software created by 3D Systems. The format is used to save and share surface-rendered 3D images and also for 3D printing.' \n", + "Data term 'U3D' has def 'U3D (Universal 3D) is a compressed file format and data structure for 3D computer graphics. It contains 3D model information such as triangle meshes, lighting, shading, motion data, lines and points with color and structure.' \n", + "Data term 'Texture file format' has def 'Bitmap image format used for storing textures.' \n", + "Data term 'MPEG-4' has def 'A digital multimedia container format most commonly used to store video and audio.' \n", + "Data term 'pickle' has def 'Format used by Python pickle module for serializing and de-serializing a Python object structure.' \n", + "Data term 'NumPy format' has def 'The standard binary file format used by NumPy - a fundamental package for scientific computing with Python - for persisting a single arbitrary NumPy array on disk. The format stores all of the shape and dtype information necessary to reconstruct the array correctly.' \n", + "Data term 'SimTools repertoire file format' has def 'Format of repertoire (archive) files that can be read by SimToolbox (a MATLAB toolbox for structured illumination fluorescence microscopy) or alternatively extracted with zip file archiver software.' \n", + "Data term 'Zstandard format' has def 'Format used by the Zstandard real-time compression algorithm.' \n", + "Data term 'Format (by type of data)' has def 'A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented.' \n", + "Data term 'Sequence record format' has def 'Data format for a molecular sequence record.' \n", + "Data term 'Sequence trace format' has def 'Format for sequence trace data (i.e. including base call information).' \n", + "Data term 'FASTQ-like format' has def 'A format resembling FASTQ short read format.' \n", + "Data term 'EMBL-like format' has def 'A format resembling EMBL entry (plain text) format.' \n", + "Data term 'FASTA-like' has def 'A format resembling FASTA format.' \n", + "Data term 'uniprotkb-like format' has def 'A sequence format resembling uniprotkb entry format.' \n", + "Data term 'UniProtKB RDF' has def 'UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML).' \n", + "Data term 'Sequence record format (text)' has def 'Data format for a molecular sequence record (text).' \n", + "Data term 'Sequence record format (XML)' has def 'Data format for a molecular sequence record (XML).' \n", + "Data term 'GenBank-like format' has def 'A format resembling GenBank entry (plain text) format.' \n", + "Data term 'BioJSON (BioXSD)' has def 'BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming.' \n", + "Data term 'BioYAML' has def 'BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editing, and object-oriented programming.' \n", + "Data term 'Sequence feature annotation format' has def 'Data format for molecular sequence feature information.' \n", + "Data term 'Sequence feature table format' has def 'Format for a sequence feature table.' \n", + "Data term 'Sequence feature table format (text)' has def 'Text format for a sequence feature table.' \n", + "Data term 'Sequin format' has def 'A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries).' \n", + "Data term 'Sequence feature table format (XML)' has def 'XML format for a sequence feature table.' \n", + "Data term 'Sequence annotation track format' has def 'Format of a sequence annotation track.' \n", + "Data term 'BioJSON (Jalview)' has def 'BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench.' \n", + "Data term 'Alignment format' has def 'Data format for molecular sequence alignment information.' \n", + "Data term 'Alignment format (text)' has def 'Text format for molecular sequence alignment information.' \n", + "Data term 'pair' has def 'EMBOSS simple sequence pairwise alignment format.' \n", + "Data term 'BLC' has def 'A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) package.' \n", + "Data term 'PO' has def 'PO is the output format of Partial Order Alignment program (POA) performing Multiple Sequence Alignment (MSA).' \n", + "Data term 'Alignment format (XML)' has def 'XML format for molecular sequence alignment information.' \n", + "Data term 'Alignment format (pair only)' has def 'Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.' \n", + "Data term 'Phylogenetic tree format' has def 'Data format for a phylogenetic tree.' \n", + "Data term 'Phylogenetic tree format (text)' has def 'Text format for a phylogenetic tree.' \n", + "Data term 'Phylogenetic tree format (XML)' has def 'XML format for a phylogenetic tree.' \n", + "Data term 'Biological pathway or network format' has def 'Data format for a biological pathway or network.' \n", + "Data term 'BioPAX' has def 'BioPAX is an exchange format for pathway data, with its data model defined in OWL.' \n", + "Data term 'sif' has def 'SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape.' \n", + "Data term 'Sequence-profile alignment format' has def 'Data format for a sequence-profile alignment.' \n", + "Data term 'Article format' has def 'Data format for a full-text scientific article.' \n", + "Data term 'Text mining report format' has def 'Data format of a report from text mining.' \n", + "Data term 'Enzyme kinetics report format' has def 'Data format for reports on enzyme kinetics.' \n", + "Data term 'Chemical data format' has def 'Format of a report on a chemical compound.' \n", + "Data term 'cif' has def 'Crystallographic Information File (CIF) is a data exchange standard file format for Crystallographic Information and related Structural Science data.' \n", + "Data term 'Gene annotation format' has def 'Format of a report on a particular locus, gene, gene system or groups of genes.' \n", + "Data term 'Workflow format' has def 'Format of a workflow.' \n", + "Data term 'KNIME datatable format' has def 'Data table formatted such that it can be passed/streamed within the KNIME platform.' \n", + "Data term 'CWL' has def 'Common Workflow Language (CWL) format for description of command-line tools and workflows.' \n", + "Data term 'Tertiary structure format' has def 'Data format for a molecular tertiary structure.' \n", + "Data term 'PDB database entry format' has def 'Format of an entry (or part of an entry) from the PDB database.' \n", + "Data term 'Chemical formula format' has def 'Text format of a chemical formula.' \n", + "Data term 'Phylogenetic character data format' has def 'Format of raw (unplotted) phylogenetic data.' \n", + "Data term 'Phylogenetic continuous quantitative character format' has def 'Format of phylogenetic continuous quantitative character data.' \n", + "Data term 'Phylogenetic discrete states format' has def 'Format of phylogenetic discrete states data.' \n", + "Data term 'Phylogenetic tree report (cliques) format' has def 'Format of phylogenetic cliques data.' \n", + "Data term 'Phylogenetic tree report (invariants) format' has def 'Format of phylogenetic invariants data.' \n", + "Data term 'Phylogenetic tree report (tree distances) format' has def 'Format for phylogenetic tree distance data.' \n", + "Data term 'Protein family report format' has def 'Format for reports on a protein family.' \n", + "Data term 'Protein interaction format' has def 'Format for molecular interaction data.' \n", + "Data term 'Sequence assembly format' has def 'Format for sequence assembly data.' \n", + "Data term 'Sequence assembly format (text)' has def 'Text format for sequence assembly data.' \n", + "Data term 'Gene expression report format' has def 'Format of a file of gene expression data, e.g. a gene expression matrix or profile.' \n", + "Data term 'Map format' has def 'Format of a map of (typically one) molecular sequence annotated with features.' \n", + "Data term 'Nucleic acid features (primers) format' has def 'Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence.' \n", + "Data term 'Protein report format' has def 'Format of a report of general information about a specific protein.' \n", + "Data term 'Protein structure report (quality evaluation) format' has def 'Format of a report on the quality of a protein three-dimensional model.' \n", + "Data term 'Database hits (sequence) format' has def 'Format of a report on sequence hits and associated data from searching a sequence database.' \n", + "Data term 'Sequence distance matrix format' has def 'Format of a matrix of genetic distances between molecular sequences.' \n", + "Data term 'Sequence motif format' has def 'Format of a sequence motif.' \n", + "Data term 'Sequence profile format' has def 'Format of a sequence profile.' \n", + "Data term 'Hidden Markov model format' has def 'Format of a hidden Markov model.' \n", + "Data term 'Dirichlet distribution format' has def 'Data format of a dirichlet distribution.' \n", + "Data term 'HMM emission and transition counts format' has def 'Data format for the emission and transition counts of a hidden Markov model.' \n", + "Data term 'RNA secondary structure format' has def 'Format for secondary structure (predicted or real) of an RNA molecule.' \n", + "Data term 'Protein secondary structure format' has def 'Format for secondary structure (predicted or real) of a protein molecule.' \n", + "Data term 'Sequence range format' has def 'Format used to specify range(s) of sequence positions.' \n", + "Data term 'Sequence features (repeats) format' has def 'Format used for map of repeats in molecular (typically nucleotide) sequences.' \n", + "Data term 'Nucleic acid features (restriction sites) format' has def 'Format used for report on restriction enzyme recognition sites in nucleotide sequences.' \n", + "Data term 'Sequence cluster format' has def 'Format used for clusters of molecular sequences.' \n", + "Data term 'Sequence cluster format (protein)' has def 'Format used for clusters of protein sequences.' \n", + "Data term 'Sequence cluster format (nucleic acid)' has def 'Format used for clusters of nucleotide sequences.' \n", + "Data term 'Ontology format' has def 'Format used for ontologies.' \n", + "Data term 'OBO format' has def 'A serialisation format conforming to the Open Biomedical Ontologies (OBO) model.' \n", + "Data term 'OWL format' has def 'A serialisation format conforming to the Web Ontology Language (OWL) model.' \n", + "Data term 'RDF format' has def 'A serialisation format conforming to the Resource Description Framework (RDF) model.' \n", + "Data term 'JSON-LD' has def 'JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON.' \n", + "Data term 'Open Annotation format' has def 'A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD.' \n", + "Data term 'Raw sequence format' has def 'Format of a raw molecular sequence (i.e. the alphabet used).' \n", + "Data term 'Bibliographic reference format' has def 'Format of a bibliographic reference.' \n", + "Data term 'Sequence variation annotation format' has def 'Format of sequence variation annotation.' \n", + "Data term 'Matrix format' has def 'Format of a matrix (array) of numerical values.' \n", + "Data term 'Amino acid index format' has def 'Data format for an amino acid index.' \n", + "Data term '3D-1D scoring matrix format' has def 'Format of a matrix of 3D-1D scores (amino acid environment probabilities).' \n", + "Data term 'MAT' has def 'Binary format used by MATLAB files to store workspace variables.' \n", + "Data term 'Protein domain classification format' has def 'Format of data concerning the classification of the sequences and/or structures of protein structural domain(s).' \n", + "Data term 'Raw SCOP domain classification format' has def 'Format of raw SCOP domain classification data files.' \n", + "Data term 'Raw CATH domain classification format' has def 'Format of raw CATH domain classification data files.' \n", + "Data term 'CATH domain report format' has def 'Format of summary of domain classification information for a CATH domain.' \n", + "Data term 'Biological pathway or network report format' has def 'Data format for a report of information derived from a biological pathway or network.' \n", + "Data term 'Experiment annotation format' has def 'Data format for annotation on a laboratory experiment.' \n", + "Data term 'Microarray experiment data format' has def 'Format for information about a microarray experimental per se (not the data generated from that experiment).' \n", + "Data term 'Mass spectrometry data format' has def 'Format for mass pectra and derived data, include peptide sequences etc.' \n", + "Data term 'MGF' has def 'Mascot Generic Format. Encodes multiple MS/MS spectra in a single file.' \n", + "Data term 'dta' has def 'Spectral data format file where each spectrum is written to a separate file.' \n", + "Data term 'pkl' has def 'Spectral data file similar to dta.' \n", + "Data term 'mzXML' has def 'Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology.' \n", + "Data term 'MSF' has def 'Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software.' \n", + "Data term 'Individual genetic data format' has def 'Data format for a metadata on an individual and their genetic data.' \n", + "Data term 'Data index format' has def 'Format of a data index of some type.' \n", + "Data term 'Document format' has def 'Format of documents including word processor, spreadsheet and presentation.' \n", + "Data term 'Image format' has def 'Format used for images and image metadata.' \n", + "Data term 'Vega' has def 'Vega is a visualization grammar, a declarative language for creating, saving, and sharing interactive visualization designs. With Vega, you can describe the visual appearance and interactive behavior of a visualization in a JSON format, and generate web-based views using Canvas or SVG.' \n", + "Data term 'Vega-lite' has def 'Vega-Lite is a high-level grammar of interactive graphics. It provides a concise JSON syntax for rapidly generating visualizations to support analysis. Vega-Lite specifications can be compiled to Vega specifications.' \n", + "Data term 'Sequence quality report format (text)' has def 'Textual report format for sequence quality for reports from sequencing machines.' \n", + "Data term 'Graph format' has def 'Data format for graph data.' \n", + "Data term 'xgmml' has def 'XML-based format used to store graph descriptions within Galaxy.' \n", + "Data term 'Biodiversity data format' has def 'Data format for biodiversity data.' \n", + "Data term 'ABCD format' has def 'Exchange format of the Access to Biological Collections Data (ABCD) Schema; a standard for the access to and exchange of data about specimens and observations (primary biodiversity data).' \n", + "Data term 'Linked data format' has def 'A linked data format enables publishing structured data as linked data (Linked Data), so that the data can be interlinked and become more useful through semantic queries.' \n", + "Data term 'Annotated text format' has def 'Data format of an annotated text, e.g. with recognised entities, concepts, and relations.' \n", + "Data term 'PubAnnotation format' has def 'JSON format of annotated scientific text used by PubAnnotations and other tools.' \n", + "Data term 'Query language' has def 'A query language (format) for structured database queries.' \n", + "Data term 'NMR data format' has def 'Data format for raw data from a nuclear magnetic resonance (NMR) spectroscopy experiment.' \n", + "Data term 'Raw microarray data format' has def 'Data format for raw microarray data.' \n", + "Data term 'NLP format' has def 'Data format used in Natural Language Processing.' \n", + "Data term 'NLP annotation format' has def 'An NLP format used for annotated textual documents.' \n", + "Data term 'NLP corpus format' has def 'NLP format used by a specific type of corpus (collection of texts).' \n", + "Data term 'RNA annotation format' has def 'A \"placeholder\" concept for formats of annotated RNA data, including e.g. microRNA and RNA-Seq data.' \n", + "Data term 'Trajectory format' has def 'File format to store trajectory information for a 3D structure .' \n", + "Data term 'Trajectory format (binary)' has def 'Binary file format to store trajectory information for a 3D structure .' \n", + "Data term 'Trajectory format (text)' has def 'Textual file format to store trajectory information for a 3D structure .' \n", + "Data term 'Topology format' has def 'Format of topology files; containing the static information of a structure molecular system that is needed for a molecular simulation.' \n", + "Data term 'FF parameter format' has def 'Format of force field parameter files, which store the set of parameters (charges, masses, radii, bond lengths, bond dihedrals, etc.) that are essential for the proper description and simulation of a molecular system.' \n", + "Data term 'JSON' has def 'JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs.' \n", + "Data term 'BioSimulators format for the specifications of biosimulation tools' has def 'Format for describing the capabilities of a biosimulation tool including the modeling frameworks, simulation algorithms, and modeling formats that it supports, as well as metadata such as a list of the interfaces, programming languages, and operating systems supported by the tool; a link to download the tool; a list of the authors of the tool; and the license to the tool.' \n", + "Data term 'YAML' has def 'YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language.' \n" + ] + } + ], + "source": [ + "## Query for format with no definition (ERROR level)\n", + "query = \"\"\"\n", + "PREFIX edam: \n", + "PREFIX oboInOwl: \n", + "\n", + "SELECT ?term ?concept ?def WHERE {\n", + " ?concept rdfs:subClassOf+ edam:format_1915 ;\n", + " rdfs:label ?term ;\n", + " \n", + " oboInOwl:hasDefinition ?def .\n", + "\n", + "}\n", + "\"\"\"\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Format term '{r['term']}' has def '{r['def']}' \") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-29T15:42:02.030054Z", + "start_time": "2024-02-29T15:42:01.964824Z" + } + }, + "execution_count": 42 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "ID hybrid 'http://edamontology.org/data_1036' 'TIGR identifier' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2112' 'FlyBase primary identifier' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2174' 'FlyBase secondary identifier' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_1154' 'KEGG object identifier' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2102' 'KEGG organism code' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_1891' 'iHOP symbol' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2104' 'BioCyc ID' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_1157' 'Pathway ID (BioCyc)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2105' 'Compound ID (BioCyc)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2106' 'Reaction ID (BioCyc)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2107' 'Enzyme ID (BioCyc)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2113' 'WormBase identifier' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_1091' 'WormBase name' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_1092' 'WormBase class' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2367' 'ASTD ID' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2368' 'ASTD ID (exon)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2369' 'ASTD ID (intron)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2370' 'ASTD ID (polya)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2371' 'ASTD ID (tss)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2380' 'CABRI accession' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2387' 'TAIR accession' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2388' 'TAIR accession (At gene)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_1033' 'Ensembl gene ID' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2398' 'Ensembl protein ID' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2725' 'Ensembl transcript ID' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_3270' 'Ensembl gene tree ID' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_1901' 'Locus ID (SGD)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2639' 'PubChem ID' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2917' 'ConsensusPathDB identifier' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2345' 'Pathway ID (ConsensusPathDB)' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2776' 'ConsensusPathDB entity ID' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_2777' 'ConsensusPathDB entity name' has regex 'None' \n", + "ID hybrid 'http://edamontology.org/data_3274' 'MGI accession' has regex 'None' \n" + ] + } + ], + "source": [ + "## Query for hybrid ID with no regex (WARNING level) (does this apply to all sorts of IDs?)\n", + "query = \"\"\"\n", + "PREFIX edam: \n", + "PREFIX oboInOwl: \n", + "\n", + "SELECT ?term ?concept ?regex WHERE {\n", + " ?concept rdfs:subClassOf+ edam:data_2109 ;\n", + " rdfs:label ?term .\n", + " \n", + " FILTER NOT EXISTS { \n", + " ?concept edam:regex ?regex \n", + " } .\n", "\n", + "}\n", + "\"\"\"\n", "results = kg.query(query)\n", "\n", "for r in results :\n", - " print(f\"Topic '{r['term']}' has no 'seeAlso' property.\") " + " print(f\"ID hybrid '{r['concept']}' '{r['term']}' has regex '{r['regex']}' \") " ], "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-30T16:27:49.429975Z", - "start_time": "2024-01-30T16:27:49.380777Z" + "end_time": "2024-02-29T16:39:48.208557Z", + "start_time": "2024-02-29T16:39:48.157318Z" } }, - "execution_count": 9 + "execution_count": 57 + }, + { + "cell_type": "markdown", + "source": [ + "## Queries from Caseologue" + ], + "metadata": { + "collapsed": false + } }, { "cell_type": "code", @@ -449,6 +1590,13 @@ }, "execution_count": 10 }, + { + "cell_type": "markdown", + "source": [], + "metadata": { + "collapsed": false + } + }, { "cell_type": "code", "outputs": [], @@ -685,8 +1833,8 @@ "\n", "results = kg.query(query)\n", "\n", - "for r in results :\n", - " print(f\"Topic '{r['term']}' has no exactSynonym.\") " + "#for r in results :\n", + " #print(f\"Topic '{r['term']}' has no exactSynonym.\") " ], "metadata": { "collapsed": false, @@ -696,6 +1844,16902 @@ } }, "execution_count": 12 + }, + { + "cell_type": "markdown", + "source": [ + "Queries from Caseologue" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "PREFIX obo: \n", + "PREFIX owl: \n", + "PREFIX rdfs: \n", + "PREFIX rdf: \n", + "PREFIX oboInOwl: \n", + "PREFIX edam:\n", + "PREFIX xsd: \n", + "\n", + "SELECT DISTINCT ?entity ?label WHERE {\n", + " \n", + " ?entity a owl:Class .\n", + " ?entity rdfs:label ?label .\n", + " FILTER NOT EXISTS { ?entity owl:deprecated true }\n", + " \n", + " FILTER NOT EXISTS {\n", + " FILTER REGEX(str(?entity), \"^http://edamontology.org/(data|topic|operation|format)_[0-9]{4}$\")\n", + " }\n", + " FILTER ( ?entity != )\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T16:49:01.045260Z", + "start_time": "2024-02-13T16:49:00.721194Z" + } + }, + "execution_count": 11 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Entity 'http://edamontology.org/topic_3068' - Label 'Literature and language'\n", + "Entity 'http://edamontology.org/topic_0219' - Label 'Data submission, annotation, and curation'\n", + "Entity 'http://edamontology.org/topic_3345' - Label 'Data identity and mapping'\n", + "Entity 'http://edamontology.org/topic_3923' - Label 'Genome resequencing'\n", + "Entity 'http://edamontology.org/topic_3524' - Label 'Simulation experiment'\n", + "Entity 'http://edamontology.org/topic_3511' - Label 'Nucleic acid sites, features and motifs'\n", + "Entity 'http://edamontology.org/topic_0123' - Label 'Protein properties'\n", + "Entity 'http://edamontology.org/topic_3510' - Label 'Protein sites, features and motifs'\n", + "Entity 'http://edamontology.org/topic_0157' - Label 'Sequence composition, complexity and repeats'\n", + "Entity 'http://edamontology.org/topic_0632' - Label 'Probes and primers'\n", + "Entity 'http://edamontology.org/topic_0160' - Label 'Sequence sites, features and motifs'\n", + "Entity 'http://edamontology.org/topic_3892' - Label 'Biomolecular simulation'\n", + "Entity 'http://edamontology.org/topic_3374' - Label 'Biotherapeutics'\n", + "Entity 'http://edamontology.org/topic_3393' - Label 'Quality affairs'\n" + ] + } + ], + "source": [ + "#Query aim = “check for missing wikipedia link in topic ”\n", + "\n", + "query=\"\"\"\n", + "PREFIX obo: \n", + "PREFIX owl: \n", + "PREFIX rdfs: \n", + "PREFIX rdf: \n", + "PREFIX oboInOwl: \n", + "PREFIX edam:\n", + "PREFIX xsd: \n", + "\n", + "SELECT DISTINCT ?entity ?label ?seealso WHERE {\n", + " ?entity rdfs:subClassOf+ .\n", + " ?entity rdfs:label ?label .\n", + " \n", + " FILTER NOT EXISTS {\n", + " ?entity rdfs:seeAlso ?seealso .\n", + " FILTER (regex(str(?seealso), \"wikipedia\", \"i\")) .\n", + " }\n", + "}\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T16:50:37.407410Z", + "start_time": "2024-02-13T16:50:37.369446Z" + } + }, + "execution_count": 12 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Entity 'http://edamontology.org/data_0005' - Label 'Resource type'\n", + "Entity 'http://edamontology.org/data_0007' - Label 'Tool'\n", + "Entity 'http://edamontology.org/data_0581' - Label 'Database'\n", + "Entity 'http://edamontology.org/data_0583' - Label 'Directory metadata'\n", + "Entity 'http://edamontology.org/data_0831' - Label 'MeSH vocabulary'\n", + "Entity 'http://edamontology.org/data_0832' - Label 'HGNC vocabulary'\n", + "Entity 'http://edamontology.org/data_0835' - Label 'UMLS vocabulary'\n", + "Entity 'http://edamontology.org/data_0843' - Label 'Database entry'\n", + "Entity 'http://edamontology.org/data_0848' - Label 'Raw sequence'\n", + "Entity 'http://edamontology.org/data_0851' - Label 'Sequence mask character'\n", + "Entity 'http://edamontology.org/data_0852' - Label 'Sequence mask type'\n", + "Entity 'http://edamontology.org/data_0853' - Label 'DNA sense specification'\n", + "Entity 'http://edamontology.org/data_0854' - Label 'Sequence length specification'\n", + "Entity 'http://edamontology.org/data_0855' - Label 'Sequence metadata'\n", + "Entity 'http://edamontology.org/data_0859' - Label 'Sequence signature model'\n", + "Entity 'http://edamontology.org/data_0861' - Label 'Sequence alignment (words)'\n", + "Entity 'http://edamontology.org/data_0864' - Label 'Sequence alignment parameter'\n", + "Entity 'http://edamontology.org/data_0866' - Label 'Sequence alignment metadata'\n", + "Entity 'http://edamontology.org/data_0868' - Label 'Profile-profile alignment'\n", + "Entity 'http://edamontology.org/data_0869' - Label 'Sequence-profile alignment'\n", + "Entity 'http://edamontology.org/data_0875' - Label 'Protein topology'\n", + "Entity 'http://edamontology.org/data_0876' - Label 'Protein features report (secondary structure)'\n", + "Entity 'http://edamontology.org/data_0877' - Label 'Protein features report (super-secondary)'\n", + "Entity 'http://edamontology.org/data_0879' - Label 'Secondary structure alignment metadata (protein)'\n", + "Entity 'http://edamontology.org/data_0882' - Label 'Secondary structure alignment metadata (RNA)'\n", + "Entity 'http://edamontology.org/data_0884' - Label 'Tertiary structure record'\n", + "Entity 'http://edamontology.org/data_0885' - Label 'Structure database search results'\n", + "Entity 'http://edamontology.org/data_0891' - Label 'Sequence-3D profile alignment'\n", + "Entity 'http://edamontology.org/data_0894' - Label 'Amino acid annotation'\n", + "Entity 'http://edamontology.org/data_0895' - Label 'Peptide annotation'\n", + "Entity 'http://edamontology.org/data_0899' - Label 'Protein structural motifs and surfaces'\n", + "Entity 'http://edamontology.org/data_0900' - Label 'Protein domain classification'\n", + "Entity 'http://edamontology.org/data_0901' - Label 'Protein features report (domains)'\n", + "Entity 'http://edamontology.org/data_0902' - Label 'Protein architecture report'\n", + "Entity 'http://edamontology.org/data_0903' - Label 'Protein folding report'\n", + "Entity 'http://edamontology.org/data_0904' - Label 'Protein features (mutation)'\n", + "Entity 'http://edamontology.org/data_0911' - Label 'Nucleotide base annotation'\n", + "Entity 'http://edamontology.org/data_0917' - Label 'Gene classification'\n", + "Entity 'http://edamontology.org/data_0918' - Label 'DNA variation'\n", + "Entity 'http://edamontology.org/data_0923' - Label 'PCR experiment report'\n", + "Entity 'http://edamontology.org/data_0931' - Label 'Microarray experiment report'\n", + "Entity 'http://edamontology.org/data_0932' - Label 'Oligonucleotide probe data'\n", + "Entity 'http://edamontology.org/data_0933' - Label 'SAGE experimental data'\n", + "Entity 'http://edamontology.org/data_0934' - Label 'MPSS experimental data'\n", + "Entity 'http://edamontology.org/data_0935' - Label 'SBS experimental data'\n", + "Entity 'http://edamontology.org/data_0936' - Label 'Sequence tag profile (with gene assignment)'\n", + "Entity 'http://edamontology.org/data_0941' - Label 'Electron microscopy model'\n", + "Entity 'http://edamontology.org/data_0946' - Label 'Pathway or network annotation'\n", + "Entity 'http://edamontology.org/data_0947' - Label 'Biological pathway map'\n", + "Entity 'http://edamontology.org/data_0948' - Label 'Data resource definition'\n", + "Entity 'http://edamontology.org/data_0952' - Label 'EMBOSS database resource definition'\n", + "Entity 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"Entity 'http://edamontology.org/topic_2847' - Label 'Disease (specific)'\n", + "Entity 'http://edamontology.org/topic_2867' - Label 'VNTR'\n", + "Entity 'http://edamontology.org/topic_2868' - Label 'Microsatellites'\n", + "Entity 'http://edamontology.org/topic_2869' - Label 'RFLP'\n", + "Entity 'http://edamontology.org/topic_2953' - Label 'Nucleic acid design'\n", + "Entity 'http://edamontology.org/topic_3032' - Label 'Primer or probe design'\n", + "Entity 'http://edamontology.org/topic_3038' - Label 'Structure databases'\n", + "Entity 'http://edamontology.org/topic_3039' - Label 'Nucleic acid structure'\n", + "Entity 'http://edamontology.org/topic_3041' - Label 'Sequence databases'\n", + "Entity 'http://edamontology.org/topic_3042' - Label 'Nucleic acid sequences'\n", + "Entity 'http://edamontology.org/topic_3043' - Label 'Protein sequences'\n", + "Entity 'http://edamontology.org/topic_3044' - Label 'Protein interaction networks'\n", + "Entity 'http://edamontology.org/topic_3048' - Label 'Mammals'\n", + "Entity 'http://edamontology.org/topic_3052' - Label 'Sequence clusters and classification'\n", + "Entity 'http://edamontology.org/topic_3060' - Label 'Regulatory RNA'\n", + "Entity 'http://edamontology.org/topic_3061' - Label 'Documentation and help'\n", + "Entity 'http://edamontology.org/topic_3062' - Label 'Genetic organisation'\n", + "Entity 'http://edamontology.org/topic_3072' - Label 'Sequence feature detection'\n", + "Entity 'http://edamontology.org/topic_3073' - Label 'Nucleic acid feature detection'\n", + "Entity 'http://edamontology.org/topic_3074' - Label 'Protein feature detection'\n", + "Entity 'http://edamontology.org/topic_3075' - Label 'Biological system modelling'\n", + "Entity 'http://edamontology.org/topic_3078' - Label 'Genes and proteins resources'\n", + "Entity 'http://edamontology.org/topic_3118' - Label 'Protein topological domains'\n", + "Entity 'http://edamontology.org/topic_3123' - Label 'Expression signals'\n", + "Entity 'http://edamontology.org/topic_3126' - Label 'Nucleic acid repeats'\n", + "Entity 'http://edamontology.org/topic_3135' - Label 'Signal or transit peptide'\n", + "Entity 'http://edamontology.org/topic_3139' - Label 'Sequence tagged sites'\n", + "Entity 'http://edamontology.org/topic_3171' - Label 'DNA methylation'\n", + "Entity 'http://edamontology.org/topic_3177' - Label 'DNA-Seq'\n", + "Entity 'http://edamontology.org/topic_3178' - Label 'RNA-Seq alignment'\n", + "Entity 'http://edamontology.org/topic_3323' - Label 'Metabolic disease'\n", + "Entity 'http://edamontology.org/topic_3346' - Label 'Sequence search'\n", + "Entity 'http://edamontology.org/topic_3413' - Label 'Infectious tropical disease'\n", + "Entity 'http://edamontology.org/topic_3514' - Label 'Protein-ligand interactions'\n", + "Entity 'http://edamontology.org/topic_3515' - Label 'Protein-drug interactions'\n", + "Entity 'http://edamontology.org/topic_3521' - Label '2D PAGE experiment'\n", + "Entity 'http://edamontology.org/topic_3522' - Label 'Northern blot experiment'\n", + "Entity 'http://edamontology.org/topic_3525' - Label 'Protein-nucleic acid interactions'\n", + "Entity 'http://edamontology.org/topic_3526' - Label 'Protein-protein interactions'\n", + "Entity 'http://edamontology.org/topic_3527' - Label 'Cellular process pathways'\n", + "Entity 'http://edamontology.org/topic_3528' - Label 'Disease pathways'\n", + "Entity 'http://edamontology.org/topic_3529' - Label 'Environmental information processing pathways'\n", + "Entity 'http://edamontology.org/topic_3530' - Label 'Genetic information processing pathways'\n", + "Entity 'http://edamontology.org/topic_3531' - Label 'Protein super-secondary structure'\n", + "Entity 'http://edamontology.org/topic_3533' - Label 'Protein active sites'\n", + "Entity 'http://edamontology.org/topic_3535' - Label 'Protein-nucleic acid binding sites'\n", + "Entity 'http://edamontology.org/topic_3536' - Label 'Protein cleavage sites'\n", + "Entity 'http://edamontology.org/topic_3537' - Label 'Protein chemical modifications'\n", + "Entity 'http://edamontology.org/topic_3539' - Label 'Protein domains'\n", + "Entity 'http://edamontology.org/topic_3540' - Label 'Protein key folding sites'\n", + "Entity 'http://edamontology.org/topic_3541' - Label 'Protein post-translational modifications'\n", + "Entity 'http://edamontology.org/topic_3543' - Label 'Protein sequence repeats'\n", + "Entity 'http://edamontology.org/topic_3544' - Label 'Protein signal peptides'\n", + "Entity 'http://www.geneontology.org/formats/oboInOwl#ObsoleteClass' - Label 'Obsolete concept (EDAM)'\n" + ] + } + ], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?label WHERE {\n", + "\n", + " ?entity a owl:Class;\n", + " owl:deprecated true .\n", + " FILTER NOT EXISTS { ?entity oboInOwl:replacedBy|oboInOwl:consider ?repl1 .} \n", + " ?entity rdfs:label ?label .\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T16:53:27.979393Z", + "start_time": "2024-02-13T16:53:27.963669Z" + } + }, + "execution_count": 14 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Entity 'http://edamontology.org/data_2539' - Label 'Alignment data'\n", + "Entity 'http://edamontology.org/topic_0747' - Label 'Nucleic acid sites and features'\n", + "Entity 'http://edamontology.org/topic_0748' - Label 'Protein sites and features'\n", + "Entity 'http://edamontology.org/topic_0751' - Label 'Phosphorylation sites'\n", + "Entity 'http://edamontology.org/topic_2280' - Label 'Nucleic acid structure comparison'\n" + ] + } + ], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?label ?property ?replacement WHERE {\n", + " VALUES ?property { oboInOwl:replacedBy\n", + " oboInOwl:consider }\n", + " ?entity ?property ?replacement .\n", + " ?entity rdfs:label ?label .\n", + " ?replacement owl:deprecated true .\n", + " \n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T16:54:56.393383Z", + "start_time": "2024-02-13T16:54:56.354587Z" + } + }, + "execution_count": 15 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Exception ignored in: >\n", + "Traceback (most recent call last):\n", + " File \"/Users/rioualen/mambaforge/lib/python3.10/site-packages/ipykernel/ipkernel.py\", line 770, in _clean_thread_parent_frames\n", + " def _clean_thread_parent_frames(\n", + "KeyboardInterrupt: \n" + ] + }, + { + "ename": "KeyboardInterrupt", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", + "\u001B[0;31mKeyboardInterrupt\u001B[0m Traceback (most recent call last)", + "Cell \u001B[0;32mIn[16], line 40\u001B[0m\n\u001B[1;32m 1\u001B[0m query\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[1;32m 2\u001B[0m \u001B[38;5;124mSELECT DISTINCT ?entity ?label ?property ?entity2 ?label2 ?property2 ?value WHERE \u001B[39m\u001B[38;5;124m{\u001B[39m\u001B[38;5;124m \u001B[39m\n\u001B[1;32m 3\u001B[0m \u001B[38;5;124m VALUES ?property \u001B[39m\u001B[38;5;124m{\u001B[39m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 35\u001B[0m \u001B[38;5;124mORDER BY ?value\u001B[39m\n\u001B[1;32m 36\u001B[0m \u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[1;32m 38\u001B[0m results \u001B[38;5;241m=\u001B[39m kg\u001B[38;5;241m.\u001B[39mquery(query)\n\u001B[0;32m---> 40\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m r \u001B[38;5;129;01min\u001B[39;00m results :\n\u001B[1;32m 41\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mEntity \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mentity\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m - Label \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mlabel\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m\"\u001B[39m) \n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/query.py:373\u001B[0m, in \u001B[0;36mResult.__iter__\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 369\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mtype \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mSELECT\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 370\u001B[0m \u001B[38;5;66;03m# this iterates over ResultRows of variable bindings\u001B[39;00m\n\u001B[1;32m 372\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_genbindings:\n\u001B[0;32m--> 373\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m b \u001B[38;5;129;01min\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_genbindings:\n\u001B[1;32m 374\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m b: \u001B[38;5;66;03m# don't add a result row in case of empty binding {}\u001B[39;00m\n\u001B[1;32m 375\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_bindings\u001B[38;5;241m.\u001B[39mappend(b)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:551\u001B[0m, in \u001B[0;36mevalDistinct\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 548\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mevalDistinct\u001B[39m(\n\u001B[1;32m 549\u001B[0m ctx: QueryContext, part: CompValue\n\u001B[1;32m 550\u001B[0m ) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m Generator[FrozenBindings, \u001B[38;5;28;01mNone\u001B[39;00m, \u001B[38;5;28;01mNone\u001B[39;00m]:\n\u001B[0;32m--> 551\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mp\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 553\u001B[0m done \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mset\u001B[39m()\n\u001B[1;32m 554\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m x \u001B[38;5;129;01min\u001B[39;00m res:\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:303\u001B[0m, in \u001B[0;36mevalPart\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 300\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalMinus(ctx, part)\n\u001B[1;32m 302\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mProject\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m--> 303\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mevalProject\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 304\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mSlice\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 305\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalSlice(ctx, part)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:561\u001B[0m, in \u001B[0;36mevalProject\u001B[0;34m(ctx, project)\u001B[0m\n\u001B[1;32m 560\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mevalProject\u001B[39m(ctx: QueryContext, project: CompValue):\n\u001B[0;32m--> 561\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mproject\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mp\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 562\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m (row\u001B[38;5;241m.\u001B[39mproject(project\u001B[38;5;241m.\u001B[39mPV) \u001B[38;5;28;01mfor\u001B[39;00m row \u001B[38;5;129;01min\u001B[39;00m res)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:312\u001B[0m, in \u001B[0;36mevalPart\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 309\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalReduced(ctx, part)\n\u001B[1;32m 311\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mOrderBy\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m--> 312\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mevalOrderBy\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 313\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mGroup\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 314\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalGroup(ctx, part)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:491\u001B[0m, in \u001B[0;36mevalOrderBy\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 489\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m e \u001B[38;5;129;01min\u001B[39;00m \u001B[38;5;28mreversed\u001B[39m(part\u001B[38;5;241m.\u001B[39mexpr):\n\u001B[1;32m 490\u001B[0m reverse \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mbool\u001B[39m(e\u001B[38;5;241m.\u001B[39morder \u001B[38;5;129;01mand\u001B[39;00m e\u001B[38;5;241m.\u001B[39morder \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mDESC\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[0;32m--> 491\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43msorted\u001B[39;49m\u001B[43m(\u001B[49m\n\u001B[1;32m 492\u001B[0m \u001B[43m \u001B[49m\u001B[43mres\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mkey\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mlambda\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mx\u001B[49m\u001B[43m:\u001B[49m\u001B[43m \u001B[49m\u001B[43m_val\u001B[49m\u001B[43m(\u001B[49m\u001B[43mvalue\u001B[49m\u001B[43m(\u001B[49m\u001B[43mx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43me\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mexpr\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mvariables\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mTrue\u001B[39;49;00m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mreverse\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mreverse\u001B[49m\n\u001B[1;32m 493\u001B[0m \u001B[43m \u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 495\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m res\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:204\u001B[0m, in \u001B[0;36mevalFilter\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 200\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mevalFilter\u001B[39m(\n\u001B[1;32m 201\u001B[0m ctx: QueryContext, part: CompValue\n\u001B[1;32m 202\u001B[0m ) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m Generator[FrozenBindings, \u001B[38;5;28;01mNone\u001B[39;00m, \u001B[38;5;28;01mNone\u001B[39;00m]:\n\u001B[1;32m 203\u001B[0m \u001B[38;5;66;03m# TODO: Deal with dict returned from evalPart!\u001B[39;00m\n\u001B[0;32m--> 204\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m c \u001B[38;5;129;01min\u001B[39;00m \u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mp\u001B[49m\u001B[43m)\u001B[49m:\n\u001B[1;32m 205\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m _ebv(\n\u001B[1;32m 206\u001B[0m part\u001B[38;5;241m.\u001B[39mexpr,\n\u001B[1;32m 207\u001B[0m c\u001B[38;5;241m.\u001B[39mforget(ctx, _except\u001B[38;5;241m=\u001B[39mpart\u001B[38;5;241m.\u001B[39m_vars) \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m part\u001B[38;5;241m.\u001B[39mno_isolated_scope \u001B[38;5;28;01melse\u001B[39;00m c,\n\u001B[1;32m 208\u001B[0m ):\n\u001B[1;32m 209\u001B[0m \u001B[38;5;28;01myield\u001B[39;00m c\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:288\u001B[0m, in \u001B[0;36mevalPart\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 286\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalFilter(ctx, part)\n\u001B[1;32m 287\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mJoin\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m--> 288\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mevalJoin\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 289\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mLeftJoin\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 290\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalLeftJoin(ctx, part)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:156\u001B[0m, in \u001B[0;36mevalJoin\u001B[0;34m(ctx, join)\u001B[0m\n\u001B[1;32m 154\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 155\u001B[0m a \u001B[38;5;241m=\u001B[39m evalPart(ctx, join\u001B[38;5;241m.\u001B[39mp1)\n\u001B[0;32m--> 156\u001B[0m b \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mset\u001B[39;49m\u001B[43m(\u001B[49m\u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mjoin\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mp2\u001B[49m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 157\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m _join(a, b)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:112\u001B[0m, in \u001B[0;36mevalBGP\u001B[0;34m(ctx, bgp)\u001B[0m\n\u001B[1;32m 109\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m AlreadyBound:\n\u001B[1;32m 110\u001B[0m \u001B[38;5;28;01mcontinue\u001B[39;00m\n\u001B[0;32m--> 112\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m x \u001B[38;5;129;01min\u001B[39;00m evalBGP(c, bgp[\u001B[38;5;241m1\u001B[39m:]):\n\u001B[1;32m 113\u001B[0m \u001B[38;5;28;01myield\u001B[39;00m x\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:112\u001B[0m, in \u001B[0;36mevalBGP\u001B[0;34m(ctx, bgp)\u001B[0m\n\u001B[1;32m 109\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m AlreadyBound:\n\u001B[1;32m 110\u001B[0m \u001B[38;5;28;01mcontinue\u001B[39;00m\n\u001B[0;32m--> 112\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m x \u001B[38;5;129;01min\u001B[39;00m evalBGP(c, bgp[\u001B[38;5;241m1\u001B[39m:]):\n\u001B[1;32m 113\u001B[0m \u001B[38;5;28;01myield\u001B[39;00m x\n", + " \u001B[0;31m[... skipping similar frames: evalBGP at line 112 (2 times)]\u001B[0m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:112\u001B[0m, in \u001B[0;36mevalBGP\u001B[0;34m(ctx, bgp)\u001B[0m\n\u001B[1;32m 109\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m AlreadyBound:\n\u001B[1;32m 110\u001B[0m \u001B[38;5;28;01mcontinue\u001B[39;00m\n\u001B[0;32m--> 112\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m x \u001B[38;5;129;01min\u001B[39;00m evalBGP(c, bgp[\u001B[38;5;241m1\u001B[39m:]):\n\u001B[1;32m 113\u001B[0m \u001B[38;5;28;01myield\u001B[39;00m x\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:84\u001B[0m, in \u001B[0;36mevalBGP\u001B[0;34m(ctx, bgp)\u001B[0m\n\u001B[1;32m 82\u001B[0m _s \u001B[38;5;241m=\u001B[39m ctx[s]\n\u001B[1;32m 83\u001B[0m _p \u001B[38;5;241m=\u001B[39m ctx[p]\n\u001B[0;32m---> 84\u001B[0m _o \u001B[38;5;241m=\u001B[39m \u001B[43mctx\u001B[49m\u001B[43m[\u001B[49m\u001B[43mo\u001B[49m\u001B[43m]\u001B[49m\n\u001B[1;32m 86\u001B[0m \u001B[38;5;66;03m# type error: Item \"None\" of \"Optional[Graph]\" has no attribute \"triples\"\u001B[39;00m\n\u001B[1;32m 87\u001B[0m \u001B[38;5;66;03m# type Argument 1 to \"triples\" of \"Graph\" has incompatible type \"Tuple[Union[str, Path, None], Union[str, Path, None], Union[str, Path, None]]\"; expected \"Tuple[Optional[Node], Optional[Node], Optional[Node]]\"\u001B[39;00m\n\u001B[1;32m 88\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m ss, sp, so \u001B[38;5;129;01min\u001B[39;00m ctx\u001B[38;5;241m.\u001B[39mgraph\u001B[38;5;241m.\u001B[39mtriples((_s, _p, _o)): \u001B[38;5;66;03m# type: ignore[union-attr, arg-type]\u001B[39;00m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/sparql.py:363\u001B[0m, in \u001B[0;36mQueryContext.__getitem__\u001B[0;34m(self, key)\u001B[0m\n\u001B[1;32m 361\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m key\n\u001B[1;32m 362\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 363\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mbindings\u001B[49m\u001B[43m[\u001B[49m\u001B[43mkey\u001B[49m\u001B[43m]\u001B[49m\n\u001B[1;32m 364\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mKeyError\u001B[39;00m:\n\u001B[1;32m 365\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/sparql.py:76\u001B[0m, in \u001B[0;36mBindings.__getitem__\u001B[0;34m(self, key)\u001B[0m\n\u001B[1;32m 74\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21m__getitem__\u001B[39m(\u001B[38;5;28mself\u001B[39m, key: \u001B[38;5;28mstr\u001B[39m) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m \u001B[38;5;28mstr\u001B[39m:\n\u001B[1;32m 75\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m key \u001B[38;5;129;01min\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_d:\n\u001B[0;32m---> 76\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_d\u001B[49m\u001B[43m[\u001B[49m\u001B[43mkey\u001B[49m\u001B[43m]\u001B[49m\n\u001B[1;32m 78\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mouter:\n\u001B[1;32m 79\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mKeyError\u001B[39;00m()\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/term.py:184\u001B[0m, in \u001B[0;36mIdentifier.__eq__\u001B[0;34m(self, other)\u001B[0m\n\u001B[1;32m 164\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 165\u001B[0m \u001B[38;5;124;03mEquality for Nodes.\u001B[39;00m\n\u001B[1;32m 166\u001B[0m \n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 180\u001B[0m \u001B[38;5;124;03mFalse\u001B[39;00m\n\u001B[1;32m 181\u001B[0m \u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 183\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mtype\u001B[39m(\u001B[38;5;28mself\u001B[39m) \u001B[38;5;241m==\u001B[39m \u001B[38;5;28mtype\u001B[39m(other):\n\u001B[0;32m--> 184\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mstr\u001B[39;49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[43m)\u001B[49m \u001B[38;5;241m==\u001B[39m \u001B[38;5;28mstr\u001B[39m(other)\n\u001B[1;32m 185\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 186\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;01mFalse\u001B[39;00m\n", + "\u001B[0;31mKeyboardInterrupt\u001B[0m: " + ] + } + ], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?label ?property ?entity2 ?label2 ?property2 ?value WHERE { \n", + " VALUES ?property {\n", + " oboInOwl:hasDefinition\n", + " oboInOwl:hasExactSynonym\n", + " oboInOwl:hasNarrowSynonym\n", + " #oboInOwl:hasBroadSynonym\n", + " #rdfs:comment\n", + " rdfs:label\n", + " }\n", + " VALUES ?property2 {\n", + " oboInOwl:hasDefinition\n", + " oboInOwl:hasExactSynonym\n", + " oboInOwl:hasNarrowSynonym\n", + " #oboInOwl:hasBroadSynonym\n", + " #rdfs:comment\n", + " #rdfs:label\n", + " }\n", + " \n", + " \n", + " ?entity a owl:Class . \n", + " ?entity2 a owl:Class . \n", + " ?entity ?property ?value .\n", + " \n", + " ?entity2 ?property2 ?value .\n", + "\n", + " #?entity2 ?property2 ?value2 . \n", + " #FILTER ( UCASE(str(?value)) = UCASE(str(?value2)) ) \n", + " \n", + " FILTER (?entity != ?entity2)\n", + " ?entity rdfs:label ?label .\n", + " ?entity2 rdfs:label ?label2 .\n", + " \n", + "}\n", + "ORDER BY ?value\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:14:02.239656Z", + "start_time": "2024-02-13T17:10:00.845188Z" + } + }, + "execution_count": 16 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "PREFIX edam:\n", + "\n", + "SELECT DISTINCT ?entity ?property ?property2 ?value ?label WHERE {\n", + " VALUES ?property {oboInOwl:hasDefinition\n", + " oboInOwl:hasExactSynonym\n", + " oboInOwl:hasNarrowSynonym\n", + " oboInOwl:hasBroadSynonym\n", + " rdfs:comment\n", + " rdfs:label\n", + " edam:documentation\n", + " }\n", + " VALUES ?property2 {oboInOwl:hasDefinition\n", + " oboInOwl:hasExactSynonym\n", + " oboInOwl:hasNarrowSynonym\n", + " oboInOwl:hasBroadSynonym\n", + " rdfs:comment\n", + " rdfs:label\n", + " edam:documentation\n", + " }\n", + "\n", + " ?entity a owl:Class . \n", + " ?entity ?property ?value .\n", + " ?entity ?property2 ?value2 .\n", + "# FILTER (?value = ?value2)\n", + " FILTER ( UCASE(str(?value)) = UCASE(str(?value2)) )\n", + "\n", + " FILTER (?property != ?property2) \n", + " ?entity rdfs:label ?label .\n", + " \n", + "}\n", + "ORDER BY ?value\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:15:39.485823Z", + "start_time": "2024-02-13T17:15:00.501498Z" + } + }, + "execution_count": 18 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?property ?value ?label WHERE {\n", + "?entity a owl:Class .\n", + "?entity ?property ?value . \n", + " FILTER REGEX (?value, \"^(.{0})$\").\n", + "?entity rdfs:label ?label\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:20:02.693754Z", + "start_time": "2024-02-13T17:20:01.684744Z" + } + }, + "execution_count": 22 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?property ?def ?label WHERE {\n", + " VALUES ?property {oboInOwl:hasDefinition} \n", + " ?entity ?property ?def .\n", + " ?entity rdfs:label ?label .\n", + "\n", + " FILTER NOT EXISTS {\n", + " FILTER REGEX(str(?def), \"['.']+$\")\n", + " }\n", + " FILTER (!isBlank(?def))\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:18:34.478418Z", + "start_time": "2024-02-13T17:18:34.209768Z" + } + }, + "execution_count": 20 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?property ?value ?label WHERE {\n", + " VALUES ?property {rdfs:label} \n", + " ?entity ?property ?value .\n", + " ?entity rdfs:label ?label .\n", + "\n", + " FILTER REGEX(str(?value), \"['.']+$\")\n", + " FILTER (!isBlank(?entity))\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:19:17.268386Z", + "start_time": "2024-02-13T17:19:17.046386Z" + } + }, + "execution_count": 21 + }, + { + "cell_type": "code", + "outputs": [ + { + "ename": "ParseException", + "evalue": "Expected SelectQuery, found ']' (at char 155), (line:7, col:1)", + "output_type": "error", + "traceback": [ + "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", + "\u001B[0;31mParseException\u001B[0m Traceback (most recent call last)", + "Cell \u001B[0;32mIn[26], line 13\u001B[0m\n\u001B[1;32m 1\u001B[0m query\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[1;32m 2\u001B[0m \u001B[38;5;124mSELECT DISTINCT ?entity ?property ?value ?label WHERE \u001B[39m\u001B[38;5;124m{\u001B[39m\n\u001B[1;32m 3\u001B[0m \u001B[38;5;124m ?entity ?property ?value .\u001B[39m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 10\u001B[0m \u001B[38;5;124mORDER BY ?entity\u001B[39m\n\u001B[1;32m 11\u001B[0m \u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[0;32m---> 13\u001B[0m results \u001B[38;5;241m=\u001B[39m \u001B[43mkg\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mquery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquery\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 15\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m r \u001B[38;5;129;01min\u001B[39;00m results :\n\u001B[1;32m 16\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mEntity \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mentity\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m - Label \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mlabel\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m\"\u001B[39m) \n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/graph.py:1565\u001B[0m, in \u001B[0;36mGraph.query\u001B[0;34m(self, query_object, processor, result, initNs, initBindings, use_store_provided, **kwargs)\u001B[0m\n\u001B[1;32m 1562\u001B[0m processor \u001B[38;5;241m=\u001B[39m plugin\u001B[38;5;241m.\u001B[39mget(processor, query\u001B[38;5;241m.\u001B[39mProcessor)(\u001B[38;5;28mself\u001B[39m)\n\u001B[1;32m 1564\u001B[0m \u001B[38;5;66;03m# type error: Argument 1 to \"Result\" has incompatible type \"Mapping[str, Any]\"; expected \"str\"\u001B[39;00m\n\u001B[0;32m-> 1565\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m result(\u001B[43mprocessor\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mquery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquery_object\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43minitBindings\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43minitNs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/processor.py:144\u001B[0m, in \u001B[0;36mSPARQLProcessor.query\u001B[0;34m(self, strOrQuery, initBindings, initNs, base, DEBUG)\u001B[0m\n\u001B[1;32m 124\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 125\u001B[0m \u001B[38;5;124;03mEvaluate a query with the given initial bindings, and initial\u001B[39;00m\n\u001B[1;32m 126\u001B[0m \u001B[38;5;124;03mnamespaces. The given base is used to resolve relative URIs in\u001B[39;00m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 140\u001B[0m \u001B[38;5;124;03m documentation.\u001B[39;00m\n\u001B[1;32m 141\u001B[0m \u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 143\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(strOrQuery, \u001B[38;5;28mstr\u001B[39m):\n\u001B[0;32m--> 144\u001B[0m strOrQuery \u001B[38;5;241m=\u001B[39m translateQuery(\u001B[43mparseQuery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mstrOrQuery\u001B[49m\u001B[43m)\u001B[49m, base, initNs)\n\u001B[1;32m 146\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalQuery(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mgraph, strOrQuery, initBindings, base)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parser.py:1542\u001B[0m, in \u001B[0;36mparseQuery\u001B[0;34m(q)\u001B[0m\n\u001B[1;32m 1539\u001B[0m q \u001B[38;5;241m=\u001B[39m q\u001B[38;5;241m.\u001B[39mdecode(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mutf-8\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 1541\u001B[0m q \u001B[38;5;241m=\u001B[39m expandUnicodeEscapes(q)\n\u001B[0;32m-> 1542\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mQuery\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mparseString\u001B[49m\u001B[43m(\u001B[49m\u001B[43mq\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mparseAll\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mTrue\u001B[39;49;00m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/pyparsing/util.py:256\u001B[0m, in \u001B[0;36m_make_synonym_function.._inner\u001B[0;34m(self, *args, **kwargs)\u001B[0m\n\u001B[1;32m 251\u001B[0m \u001B[38;5;129m@wraps\u001B[39m(fn)\n\u001B[1;32m 252\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21m_inner\u001B[39m(\u001B[38;5;28mself\u001B[39m, \u001B[38;5;241m*\u001B[39margs, \u001B[38;5;241m*\u001B[39m\u001B[38;5;241m*\u001B[39mkwargs):\n\u001B[1;32m 253\u001B[0m \u001B[38;5;66;03m# warnings.warn(\u001B[39;00m\n\u001B[1;32m 254\u001B[0m \u001B[38;5;66;03m# f\"Deprecated - use {fn.__name__}\", DeprecationWarning, stacklevel=3\u001B[39;00m\n\u001B[1;32m 255\u001B[0m \u001B[38;5;66;03m# )\u001B[39;00m\n\u001B[0;32m--> 256\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mfn\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43margs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/pyparsing/core.py:1197\u001B[0m, in \u001B[0;36mParserElement.parse_string\u001B[0;34m(self, instring, parse_all, parseAll)\u001B[0m\n\u001B[1;32m 1194\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m\n\u001B[1;32m 1195\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1196\u001B[0m \u001B[38;5;66;03m# catch and re-raise exception from here, clearing out pyparsing internal stack trace\u001B[39;00m\n\u001B[0;32m-> 1197\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m exc\u001B[38;5;241m.\u001B[39mwith_traceback(\u001B[38;5;28;01mNone\u001B[39;00m)\n\u001B[1;32m 1198\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1199\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m tokens\n", + "\u001B[0;31mParseException\u001B[0m: Expected SelectQuery, found ']' (at char 155), (line:7, col:1)" + ] + } + ], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?property ?value ?label WHERE {\n", + " ?entity ?property ?value .\n", + " ?entity rdfs:label ?label .\n", + "\n", + " #FILTER REGEX(str(?value), \"[\\\\s\\r\\n]+$\")\n", + " #FILTER (!isBlank(?entity))\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:22:06.994601Z", + "start_time": "2024-02-13T17:22:06.949433Z" + } + }, + "execution_count": 26 + }, + { + "cell_type": "code", + "outputs": [ + { + "ename": "ParseException", + "evalue": "Expected SelectQuery, found 'FILTER' (at char 126), (line:6, col:4)", + "output_type": "error", + "traceback": [ + "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", + "\u001B[0;31mParseException\u001B[0m Traceback (most recent call last)", + "Cell \u001B[0;32mIn[28], line 13\u001B[0m\n\u001B[1;32m 1\u001B[0m query\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[1;32m 2\u001B[0m \u001B[38;5;124mSELECT DISTINCT ?entity ?property ?value ?label \u001B[39m\n\u001B[1;32m 3\u001B[0m \u001B[38;5;124mWHERE \u001B[39m\u001B[38;5;124m{\u001B[39m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 10\u001B[0m \u001B[38;5;124mORDER BY ?entity\u001B[39m\n\u001B[1;32m 11\u001B[0m \u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[0;32m---> 13\u001B[0m results \u001B[38;5;241m=\u001B[39m \u001B[43mkg\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mquery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquery\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 15\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m r \u001B[38;5;129;01min\u001B[39;00m results :\n\u001B[1;32m 16\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mEntity \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mentity\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m - Label \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mlabel\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m\"\u001B[39m) \n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/graph.py:1565\u001B[0m, in \u001B[0;36mGraph.query\u001B[0;34m(self, query_object, processor, result, initNs, initBindings, use_store_provided, **kwargs)\u001B[0m\n\u001B[1;32m 1562\u001B[0m processor \u001B[38;5;241m=\u001B[39m plugin\u001B[38;5;241m.\u001B[39mget(processor, query\u001B[38;5;241m.\u001B[39mProcessor)(\u001B[38;5;28mself\u001B[39m)\n\u001B[1;32m 1564\u001B[0m \u001B[38;5;66;03m# type error: Argument 1 to \"Result\" has incompatible type \"Mapping[str, Any]\"; expected \"str\"\u001B[39;00m\n\u001B[0;32m-> 1565\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m result(\u001B[43mprocessor\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mquery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquery_object\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43minitBindings\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43minitNs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/processor.py:144\u001B[0m, in \u001B[0;36mSPARQLProcessor.query\u001B[0;34m(self, strOrQuery, initBindings, initNs, base, DEBUG)\u001B[0m\n\u001B[1;32m 124\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 125\u001B[0m \u001B[38;5;124;03mEvaluate a query with the given initial bindings, and initial\u001B[39;00m\n\u001B[1;32m 126\u001B[0m \u001B[38;5;124;03mnamespaces. The given base is used to resolve relative URIs in\u001B[39;00m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 140\u001B[0m \u001B[38;5;124;03m documentation.\u001B[39;00m\n\u001B[1;32m 141\u001B[0m \u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 143\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(strOrQuery, \u001B[38;5;28mstr\u001B[39m):\n\u001B[0;32m--> 144\u001B[0m strOrQuery \u001B[38;5;241m=\u001B[39m translateQuery(\u001B[43mparseQuery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mstrOrQuery\u001B[49m\u001B[43m)\u001B[49m, base, initNs)\n\u001B[1;32m 146\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalQuery(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mgraph, strOrQuery, initBindings, base)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parser.py:1542\u001B[0m, in \u001B[0;36mparseQuery\u001B[0;34m(q)\u001B[0m\n\u001B[1;32m 1539\u001B[0m q \u001B[38;5;241m=\u001B[39m q\u001B[38;5;241m.\u001B[39mdecode(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mutf-8\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 1541\u001B[0m q \u001B[38;5;241m=\u001B[39m expandUnicodeEscapes(q)\n\u001B[0;32m-> 1542\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mQuery\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mparseString\u001B[49m\u001B[43m(\u001B[49m\u001B[43mq\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mparseAll\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mTrue\u001B[39;49;00m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/pyparsing/util.py:256\u001B[0m, in \u001B[0;36m_make_synonym_function.._inner\u001B[0;34m(self, *args, **kwargs)\u001B[0m\n\u001B[1;32m 251\u001B[0m \u001B[38;5;129m@wraps\u001B[39m(fn)\n\u001B[1;32m 252\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21m_inner\u001B[39m(\u001B[38;5;28mself\u001B[39m, \u001B[38;5;241m*\u001B[39margs, \u001B[38;5;241m*\u001B[39m\u001B[38;5;241m*\u001B[39mkwargs):\n\u001B[1;32m 253\u001B[0m \u001B[38;5;66;03m# warnings.warn(\u001B[39;00m\n\u001B[1;32m 254\u001B[0m \u001B[38;5;66;03m# f\"Deprecated - use {fn.__name__}\", DeprecationWarning, stacklevel=3\u001B[39;00m\n\u001B[1;32m 255\u001B[0m \u001B[38;5;66;03m# )\u001B[39;00m\n\u001B[0;32m--> 256\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mfn\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43margs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/pyparsing/core.py:1197\u001B[0m, in \u001B[0;36mParserElement.parse_string\u001B[0;34m(self, instring, parse_all, parseAll)\u001B[0m\n\u001B[1;32m 1194\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m\n\u001B[1;32m 1195\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1196\u001B[0m \u001B[38;5;66;03m# catch and re-raise exception from here, clearing out pyparsing internal stack trace\u001B[39;00m\n\u001B[0;32m-> 1197\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m exc\u001B[38;5;241m.\u001B[39mwith_traceback(\u001B[38;5;28;01mNone\u001B[39;00m)\n\u001B[1;32m 1198\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1199\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m tokens\n", + "\u001B[0;31mParseException\u001B[0m: Expected SelectQuery, found 'FILTER' (at char 126), (line:6, col:4)" + ] + } + ], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?property ?value ?label \n", + "WHERE {\n", + " ?entity ?property ?value .\n", + " ?entity rdfs:label ?label . \n", + " FILTER regex(?value, \"\\n\")\n", + " FILTER (!isBlank(?entity))\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:25:17.173205Z", + "start_time": "2024-02-13T17:25:17.140331Z" + } + }, + "execution_count": 28 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Entity 'http://edamontology.org/format_1196' - Label 'SMILES'\n", + "Entity 'http://edamontology.org/format_1197' - Label 'InChI'\n", + "Entity 'http://edamontology.org/format_1197' - Label 'InChI'\n", + "Entity 'http://edamontology.org/format_1198' - Label 'mf'\n", + "Entity 'http://edamontology.org/format_1198' - Label 'mf'\n", + "Entity 'http://edamontology.org/format_1199' - Label 'InChIKey'\n", + "Entity 'http://edamontology.org/format_1199' - Label 'InChIKey'\n", + "Entity 'http://edamontology.org/format_1200' - Label 'smarts'\n", + "Entity 'http://edamontology.org/format_1200' - Label 'smarts'\n", + "Entity 'http://edamontology.org/format_1206' - Label 'unambiguous pure'\n", + "Entity 'http://edamontology.org/format_1206' - Label 'unambiguous pure'\n", + "Entity 'http://edamontology.org/format_1207' - Label 'nucleotide'\n", + "Entity 'http://edamontology.org/format_1207' - Label 'nucleotide'\n", + "Entity 'http://edamontology.org/format_1208' - Label 'protein'\n", + "Entity 'http://edamontology.org/format_1208' - Label 'protein'\n", + "Entity 'http://edamontology.org/format_1209' - Label 'consensus'\n", + "Entity 'http://edamontology.org/format_1209' - Label 'consensus'\n", + "Entity 'http://edamontology.org/format_1210' - Label 'pure nucleotide'\n", + "Entity 'http://edamontology.org/format_1210' - Label 'pure nucleotide'\n", + "Entity 'http://edamontology.org/format_1211' - Label 'unambiguous pure nucleotide'\n", + "Entity 'http://edamontology.org/format_1211' - Label 'unambiguous pure nucleotide'\n", + "Entity 'http://edamontology.org/format_1212' - Label 'dna'\n", + "Entity 'http://edamontology.org/format_1212' - Label 'dna'\n", + "Entity 'http://edamontology.org/format_1213' - Label 'rna'\n", + "Entity 'http://edamontology.org/format_1213' - Label 'rna'\n", + "Entity 'http://edamontology.org/format_1214' - Label 'unambiguous pure dna'\n", + "Entity 'http://edamontology.org/format_1214' - Label 'unambiguous pure dna'\n", + "Entity 'http://edamontology.org/format_1215' - Label 'pure dna'\n", + "Entity 'http://edamontology.org/format_1215' - Label 'pure dna'\n", + "Entity 'http://edamontology.org/format_1216' - Label 'unambiguous pure rna sequence'\n", + "Entity 'http://edamontology.org/format_1216' - Label 'unambiguous pure rna sequence'\n", + "Entity 'http://edamontology.org/format_1217' - Label 'pure rna'\n", + "Entity 'http://edamontology.org/format_1217' - Label 'pure rna'\n", + "Entity 'http://edamontology.org/format_1218' - Label 'unambiguous pure protein'\n", + "Entity 'http://edamontology.org/format_1218' - Label 'unambiguous pure protein'\n", + "Entity 'http://edamontology.org/format_1219' - Label 'pure protein'\n", + "Entity 'http://edamontology.org/format_1219' - Label 'pure protein'\n", + "Entity 'http://edamontology.org/format_1248' - Label 'EMBL feature location'\n", + "Entity 'http://edamontology.org/format_1248' - Label 'EMBL feature location'\n", + "Entity 'http://edamontology.org/format_1295' - Label 'quicktandem'\n", + "Entity 'http://edamontology.org/format_1295' - Label 'quicktandem'\n", + "Entity 'http://edamontology.org/format_1296' - Label 'Sanger inverted repeats'\n", + "Entity 'http://edamontology.org/format_1296' - Label 'Sanger inverted repeats'\n", + "Entity 'http://edamontology.org/format_1297' - Label 'EMBOSS repeat'\n", + "Entity 'http://edamontology.org/format_1297' - Label 'EMBOSS repeat'\n", + "Entity 'http://edamontology.org/format_1316' - Label 'est2genome format'\n", + "Entity 'http://edamontology.org/format_1316' - Label 'est2genome format'\n", + "Entity 'http://edamontology.org/format_1318' - Label 'restrict format'\n", + "Entity 'http://edamontology.org/format_1318' - Label 'restrict format'\n", + "Entity 'http://edamontology.org/format_1319' - Label 'restover format'\n", + "Entity 'http://edamontology.org/format_1319' - Label 'restover format'\n", + "Entity 'http://edamontology.org/format_1320' - Label 'REBASE restriction sites'\n", + "Entity 'http://edamontology.org/format_1320' - Label 'REBASE restriction sites'\n", + "Entity 'http://edamontology.org/format_1332' - Label 'FASTA search results format'\n", + "Entity 'http://edamontology.org/format_1332' - Label 'FASTA search results format'\n", + "Entity 'http://edamontology.org/format_1333' - Label 'BLAST results'\n", + "Entity 'http://edamontology.org/format_1333' - Label 'BLAST results'\n", + "Entity 'http://edamontology.org/format_1334' - Label 'mspcrunch'\n", + "Entity 'http://edamontology.org/format_1334' - Label 'mspcrunch'\n", + "Entity 'http://edamontology.org/format_1335' - Label 'Smith-Waterman format'\n", + "Entity 'http://edamontology.org/format_1335' - Label 'Smith-Waterman format'\n", + "Entity 'http://edamontology.org/format_1336' - Label 'dhf'\n", + "Entity 'http://edamontology.org/format_1336' - Label 'dhf'\n", + "Entity 'http://edamontology.org/format_1337' - Label 'lhf'\n", + "Entity 'http://edamontology.org/format_1337' - Label 'lhf'\n", + "Entity 'http://edamontology.org/format_1341' - Label 'InterPro hits format'\n", + "Entity 'http://edamontology.org/format_1341' - Label 'InterPro hits format'\n", + "Entity 'http://edamontology.org/format_1342' - Label 'InterPro protein view report format'\n", + "Entity 'http://edamontology.org/format_1342' - Label 'InterPro protein view report format'\n", + "Entity 'http://edamontology.org/format_1343' - Label 'InterPro match table format'\n", + "Entity 'http://edamontology.org/format_1343' - Label 'InterPro match table format'\n", + "Entity 'http://edamontology.org/format_1349' - Label 'HMMER Dirichlet prior'\n", + "Entity 'http://edamontology.org/format_1349' - Label 'HMMER Dirichlet prior'\n", + "Entity 'http://edamontology.org/format_1350' - Label 'MEME Dirichlet prior'\n", + "Entity 'http://edamontology.org/format_1350' - Label 'MEME Dirichlet prior'\n", + "Entity 'http://edamontology.org/format_1351' - Label 'HMMER emission and transition'\n", + "Entity 'http://edamontology.org/format_1351' - Label 'HMMER emission and transition'\n", + "Entity 'http://edamontology.org/format_1356' - Label 'prosite-pattern'\n", + "Entity 'http://edamontology.org/format_1356' - Label 'prosite-pattern'\n", + "Entity 'http://edamontology.org/format_1357' - Label 'EMBOSS sequence pattern'\n", + "Entity 'http://edamontology.org/format_1357' - Label 'EMBOSS sequence pattern'\n", + "Entity 'http://edamontology.org/format_1360' - Label 'meme-motif'\n", + "Entity 'http://edamontology.org/format_1360' - Label 'meme-motif'\n", + "Entity 'http://edamontology.org/format_1366' - Label 'prosite-profile'\n", + "Entity 'http://edamontology.org/format_1366' - Label 'prosite-profile'\n", + "Entity 'http://edamontology.org/format_1367' - Label 'JASPAR format'\n", + "Entity 'http://edamontology.org/format_1367' - Label 'JASPAR format'\n", + "Entity 'http://edamontology.org/format_1369' - Label 'MEME background Markov model'\n", + "Entity 'http://edamontology.org/format_1369' - Label 'MEME background Markov model'\n", + "Entity 'http://edamontology.org/format_1370' - Label 'HMMER format'\n", + "Entity 'http://edamontology.org/format_1370' - Label 'HMMER format'\n", + "Entity 'http://edamontology.org/format_1391' - Label 'HMMER-aln'\n", + "Entity 'http://edamontology.org/format_1391' - Label 'HMMER-aln'\n", + "Entity 'http://edamontology.org/format_1392' - Label 'DIALIGN format'\n", + "Entity 'http://edamontology.org/format_1392' - Label 'DIALIGN format'\n", + "Entity 'http://edamontology.org/format_1393' - Label 'daf'\n", + "Entity 'http://edamontology.org/format_1393' - Label 'daf'\n", + "Entity 'http://edamontology.org/format_1419' - Label 'Sequence-MEME profile alignment'\n", + "Entity 'http://edamontology.org/format_1419' - Label 'Sequence-MEME profile alignment'\n", + "Entity 'http://edamontology.org/format_1421' - Label 'HMMER profile alignment (sequences versus HMMs)'\n", + "Entity 'http://edamontology.org/format_1421' - Label 'HMMER profile alignment (sequences versus HMMs)'\n", + "Entity 'http://edamontology.org/format_1422' - Label 'HMMER profile alignment (HMM versus sequences)'\n", + "Entity 'http://edamontology.org/format_1422' - Label 'HMMER profile alignment (HMM versus sequences)'\n", + "Entity 'http://edamontology.org/format_1423' - Label 'Phylip distance matrix'\n", + "Entity 'http://edamontology.org/format_1423' - Label 'Phylip distance matrix'\n", + "Entity 'http://edamontology.org/format_1424' - Label 'ClustalW dendrogram'\n", + "Entity 'http://edamontology.org/format_1424' - Label 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"Entity 'http://www.w3.org/2002/07/owl#DeprecatedClass' - Label 'None'\n" + ] + } + ], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?label WHERE {\n", + " \n", + " ?entity a owl:Class .\n", + " OPTIONAL {?entity rdfs:label ?label .}\n", + " \n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:28:58.299173Z", + "start_time": "2024-02-13T17:28:58.179473Z" + } + }, + "execution_count": 33 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Entity 'http://edamontology.org/data_1002' - Label 'CAS number'\n", + "Entity 'http://edamontology.org/data_1003' - Label 'Chemical registry number (Beilstein)'\n", + "Entity 'http://edamontology.org/data_1004' - Label 'Chemical registry number (Gmelin)'\n", + "Entity 'http://edamontology.org/data_1027' - Label 'Gene ID (NCBI)'\n", + "Entity 'http://edamontology.org/data_1031' - Label 'Gene ID (CGD)'\n", + "Entity 'http://edamontology.org/data_1032' - Label 'Gene ID (DictyBase)'\n", + "Entity 'http://edamontology.org/data_1033' - Label 'Ensembl gene ID'\n", + "Entity 'http://edamontology.org/data_1036' - Label 'TIGR identifier'\n", + "Entity 'http://edamontology.org/data_1039' - Label 'SCOP domain identifier'\n", + "Entity 'http://edamontology.org/data_1040' - Label 'CATH domain ID'\n", + "Entity 'http://edamontology.org/data_1041' - Label 'SCOP concise classification string (sccs)'\n", + "Entity 'http://edamontology.org/data_1042' - Label 'SCOP sunid'\n", + "Entity 'http://edamontology.org/data_1043' - Label 'CATH node ID'\n", + "Entity 'http://edamontology.org/data_1066' - Label 'Sequence alignment ID'\n", + "Entity 'http://edamontology.org/data_1100' - Label 'PIR identifier'\n", + "Entity 'http://edamontology.org/data_1102' - Label 'Gramene primary identifier'\n", + "Entity 'http://edamontology.org/data_1103' - Label 'EMBL/GenBank/DDBJ ID'\n", + "Entity 'http://edamontology.org/data_1104' - Label 'Sequence cluster ID (UniGene)'\n", + "Entity 'http://edamontology.org/data_1105' - Label 'dbEST accession'\n", + "Entity 'http://edamontology.org/data_1106' - Label 'dbSNP ID'\n", + "Entity 'http://edamontology.org/data_1113' - Label 'Sequence cluster ID (COG)'\n", + "Entity 'http://edamontology.org/data_1118' - Label 'HMMER hidden Markov model ID'\n", + "Entity 'http://edamontology.org/data_1119' - Label 'JASPAR profile ID'\n", + "Entity 'http://edamontology.org/data_1123' - Label 'TreeBASE study accession number'\n", + "Entity 'http://edamontology.org/data_1124' - Label 'TreeFam accession number'\n", + "Entity 'http://edamontology.org/data_1128' - Label 'AAindex ID'\n", + "Entity 'http://edamontology.org/data_1129' - Label 'BIND accession number'\n", + "Entity 'http://edamontology.org/data_1134' - Label 'InterPro secondary accession'\n", + "Entity 'http://edamontology.org/data_1135' - Label 'Gene3D ID'\n", + "Entity 'http://edamontology.org/data_1140' - Label 'Superfamily hidden Markov model number'\n", + "Entity 'http://edamontology.org/data_1141' - Label 'TIGRFam ID'\n", + "Entity 'http://edamontology.org/data_1143' - Label 'TRANSFAC accession number'\n", + "Entity 'http://edamontology.org/data_1146' - Label 'EMDB ID'\n", + "Entity 'http://edamontology.org/data_1148' - Label 'GermOnline ID'\n", + "Entity 'http://edamontology.org/data_1149' - Label 'EMAGE ID'\n", + "Entity 'http://edamontology.org/data_1151' - Label 'HGVbase ID'\n", + "Entity 'http://edamontology.org/data_1154' - Label 'KEGG object identifier'\n", + "Entity 'http://edamontology.org/data_1157' - Label 'Pathway ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_1158' - Label 'Pathway ID (INOH)'\n", + "Entity 'http://edamontology.org/data_1159' - Label 'Pathway ID (PATIKA)'\n", + "Entity 'http://edamontology.org/data_1160' - Label 'Pathway ID (CPDB)'\n", + "Entity 'http://edamontology.org/data_1164' - Label 'MIRIAM URI'\n", + "Entity 'http://edamontology.org/data_1167' - Label 'Taverna workflow ID'\n", + "Entity 'http://edamontology.org/data_1175' - Label 'BioPax concept ID'\n", + "Entity 'http://edamontology.org/data_1177' - Label 'MeSH concept ID'\n", + "Entity 'http://edamontology.org/data_1178' - Label 'HGNC concept ID'\n", + "Entity 'http://edamontology.org/data_1180' - Label 'Plant Ontology concept ID'\n", + "Entity 'http://edamontology.org/data_1181' - Label 'UMLS concept ID'\n", + "Entity 'http://edamontology.org/data_1183' - Label 'EMAP concept ID'\n", + "Entity 'http://edamontology.org/data_1184' - Label 'ChEBI concept ID'\n", + "Entity 'http://edamontology.org/data_1185' - Label 'MGED concept ID'\n", + "Entity 'http://edamontology.org/data_1186' - Label 'myGrid concept ID'\n", + "Entity 'http://edamontology.org/data_1189' - Label 'Medline UI'\n", + "Entity 'http://edamontology.org/data_1794' - Label 'Gene ID (PlasmoDB)'\n", + "Entity 'http://edamontology.org/data_1795' - Label 'Gene ID (EcoGene)'\n", + "Entity 'http://edamontology.org/data_1796' - Label 'Gene ID (FlyBase)'\n", + "Entity 'http://edamontology.org/data_1802' - Label 'Gene ID (Gramene)'\n", + "Entity 'http://edamontology.org/data_1803' - Label 'Gene ID (Virginia microbial)'\n", + "Entity 'http://edamontology.org/data_1804' - Label 'Gene ID (SGN)'\n", + "Entity 'http://edamontology.org/data_1873' - Label 'iHOP organism ID'\n", + "Entity 'http://edamontology.org/data_1885' - Label 'Gene ID (GeneFarm)'\n", + "Entity 'http://edamontology.org/data_1886' - Label 'Blattner number'\n", + "Entity 'http://edamontology.org/data_1891' - Label 'iHOP symbol'\n", + "Entity 'http://edamontology.org/data_1896' - Label 'Locus ID (ASPGD)'\n", + "Entity 'http://edamontology.org/data_1897' - Label 'Locus ID (MGG)'\n", + "Entity 'http://edamontology.org/data_1898' - Label 'Locus ID (CGD)'\n", + "Entity 'http://edamontology.org/data_1899' - Label 'Locus ID (CMR)'\n", + "Entity 'http://edamontology.org/data_1900' - Label 'NCBI locus tag'\n", + "Entity 'http://edamontology.org/data_1901' - Label 'Locus ID (SGD)'\n", + "Entity 'http://edamontology.org/data_1902' - Label 'Locus ID (MMP)'\n", + "Entity 'http://edamontology.org/data_1903' - Label 'Locus ID (DictyBase)'\n", + "Entity 'http://edamontology.org/data_1904' - Label 'Locus ID (EntrezGene)'\n", + "Entity 'http://edamontology.org/data_1905' - Label 'Locus ID (MaizeGDB)'\n", + "Entity 'http://edamontology.org/data_1907' - Label 'Gene ID (KOME)'\n", + "Entity 'http://edamontology.org/data_1908' - Label 'Locus ID (Tropgene)'\n", + "Entity 'http://edamontology.org/data_2102' - Label 'KEGG organism code'\n", + "Entity 'http://edamontology.org/data_2104' - Label 'BioCyc ID'\n", + "Entity 'http://edamontology.org/data_2105' - Label 'Compound ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2106' - Label 'Reaction ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2107' - Label 'Enzyme ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2112' - Label 'FlyBase primary identifier'\n", + "Entity 'http://edamontology.org/data_2174' - Label 'FlyBase secondary identifier'\n", + "Entity 'http://edamontology.org/data_2209' - Label 'Mutation ID'\n", + "Entity 'http://edamontology.org/data_2220' - Label 'Sequence cluster ID (SYSTERS)'\n", + "Entity 'http://edamontology.org/data_2285' - Label 'Gene ID (MIPS)'\n", + "Entity 'http://edamontology.org/data_2290' - Label 'EMBL accession'\n", + "Entity 'http://edamontology.org/data_2292' - Label 'GenBank accession'\n", + "Entity 'http://edamontology.org/data_2293' - Label 'Gramene secondary identifier'\n", + "Entity 'http://edamontology.org/data_2297' - Label 'Gene ID (ECK)'\n", + "Entity 'http://edamontology.org/data_2298' - Label 'Gene ID (HGNC)'\n", + "Entity 'http://edamontology.org/data_2302' - Label 'STRING ID'\n", + "Entity 'http://edamontology.org/data_2314' - Label 'GI number'\n", + "Entity 'http://edamontology.org/data_2315' - Label 'NCBI version'\n", + "Entity 'http://edamontology.org/data_2325' - Label 'REBASE enzyme number'\n", + "Entity 'http://edamontology.org/data_2327' - Label 'GI number (protein)'\n", + "Entity 'http://edamontology.org/data_2345' - Label 'Pathway ID (ConsensusPathDB)'\n", + "Entity 'http://edamontology.org/data_2346' - Label 'Sequence cluster ID (UniRef)'\n", + "Entity 'http://edamontology.org/data_2347' - Label 'Sequence cluster ID (UniRef100)'\n", + "Entity 'http://edamontology.org/data_2348' - Label 'Sequence cluster ID (UniRef90)'\n", + "Entity 'http://edamontology.org/data_2349' - Label 'Sequence cluster ID (UniRef50)'\n", + "Entity 'http://edamontology.org/data_2356' - Label 'RFAM accession'\n", + "Entity 'http://edamontology.org/data_2367' - Label 'ASTD ID'\n", + "Entity 'http://edamontology.org/data_2368' - Label 'ASTD ID (exon)'\n", + "Entity 'http://edamontology.org/data_2369' - Label 'ASTD ID (intron)'\n", + "Entity 'http://edamontology.org/data_2370' - Label 'ASTD ID (polya)'\n", + "Entity 'http://edamontology.org/data_2371' - Label 'ASTD ID (tss)'\n", + "Entity 'http://edamontology.org/data_2374' - Label 'Spot serial number'\n", + "Entity 'http://edamontology.org/data_2375' - Label 'Spot ID (HSC-2DPAGE)'\n", + "Entity 'http://edamontology.org/data_2380' - Label 'CABRI accession'\n", + "Entity 'http://edamontology.org/data_2383' - Label 'EGA accession'\n", + "Entity 'http://edamontology.org/data_2385' - Label 'RefSeq accession (protein)'\n", + "Entity 'http://edamontology.org/data_2386' - Label 'EPD ID'\n", + "Entity 'http://edamontology.org/data_2387' - Label 'TAIR accession'\n", + "Entity 'http://edamontology.org/data_2388' - Label 'TAIR accession (At gene)'\n", + "Entity 'http://edamontology.org/data_2389' - Label 'UniSTS accession'\n", + "Entity 'http://edamontology.org/data_2390' - Label 'UNITE accession'\n", + "Entity 'http://edamontology.org/data_2391' - Label 'UTR accession'\n", + "Entity 'http://edamontology.org/data_2393' - Label 'mFLJ/mKIAA number'\n", + "Entity 'http://edamontology.org/data_2398' - Label 'Ensembl protein ID'\n", + "Entity 'http://edamontology.org/data_2578' - Label 'ArachnoServer ID'\n", + "Entity 'http://edamontology.org/data_2580' - Label 'BindingDB Monomer ID'\n", + "Entity 'http://edamontology.org/data_2588' - Label 'BlotBase blot ID'\n", + "Entity 'http://edamontology.org/data_2591' - Label 'Brite hierarchy ID'\n", + "Entity 'http://edamontology.org/data_2593' - Label 'BRENDA organism ID'\n", + "Entity 'http://edamontology.org/data_2639' - Label 'PubChem ID'\n", + "Entity 'http://edamontology.org/data_2700' - Label 'CATH identifier'\n", + "Entity 'http://edamontology.org/data_2701' - Label 'CATH node ID (family)'\n", + "Entity 'http://edamontology.org/data_2702' - Label 'Enzyme ID (CAZy)'\n", + "Entity 'http://edamontology.org/data_2704' - Label 'Clone ID (IMAGE)'\n", + "Entity 'http://edamontology.org/data_2709' - Label 'CleanEx entry name'\n", + "Entity 'http://edamontology.org/data_2713' - Label 'Protein ID (CORUM)'\n", + "Entity 'http://edamontology.org/data_2714' - Label 'CDD PSSM-ID'\n", + "Entity 'http://edamontology.org/data_2715' - Label 'Protein ID (CuticleDB)'\n", + "Entity 'http://edamontology.org/data_2716' - Label 'DBD ID'\n", + "Entity 'http://edamontology.org/data_2719' - Label 'dbProbe ID'\n", + "Entity 'http://edamontology.org/data_2721' - Label 'DiProDB ID'\n", + "Entity 'http://edamontology.org/data_2723' - Label 'Protein ID (DisProt)'\n", + "Entity 'http://edamontology.org/data_2725' - Label 'Ensembl transcript ID'\n", + "Entity 'http://edamontology.org/data_2729' - Label 'COGEME EST ID'\n", + "Entity 'http://edamontology.org/data_2730' - Label 'COGEME unisequence ID'\n", + "Entity 'http://edamontology.org/data_2731' - Label 'Protein family ID (GeneFarm)'\n", + "Entity 'http://edamontology.org/data_2736' - Label 'Sequence feature ID (SwissRegulon)'\n", + "Entity 'http://edamontology.org/data_2737' - Label 'FIG ID'\n", + "Entity 'http://edamontology.org/data_2738' - Label 'Gene ID (Xenbase)'\n", + "Entity 'http://edamontology.org/data_2739' - Label 'Gene ID (Genolist)'\n", + "Entity 'http://edamontology.org/data_2741' - Label 'ABS ID'\n", + "Entity 'http://edamontology.org/data_2742' - Label 'AraC-XylS ID'\n", + "Entity 'http://edamontology.org/data_2744' - Label 'Locus ID (PseudoCAP)'\n", + "Entity 'http://edamontology.org/data_2745' - Label 'Locus ID (UTR)'\n", + "Entity 'http://edamontology.org/data_2746' - Label 'MonosaccharideDB ID'\n", + "Entity 'http://edamontology.org/data_2756' - Label 'TCID'\n", + "Entity 'http://edamontology.org/data_2759' - Label 'Gene ID (VectorBase)'\n", + "Entity 'http://edamontology.org/data_2766' - Label 'HAMAP ID'\n", + "Entity 'http://edamontology.org/data_2770' - Label 'HIT ID'\n", + "Entity 'http://edamontology.org/data_2771' - Label 'HIX ID'\n", + "Entity 'http://edamontology.org/data_2772' - Label 'HPA antibody id'\n", + "Entity 'http://edamontology.org/data_2773' - Label 'IMGT/HLA ID'\n", + "Entity 'http://edamontology.org/data_2774' - Label 'Gene ID (JCVI)'\n", + "Entity 'http://edamontology.org/data_2776' - Label 'ConsensusPathDB entity ID'\n", + "Entity 'http://edamontology.org/data_2778' - Label 'CCAP strain number'\n", + "Entity 'http://edamontology.org/data_2780' - Label 'Stock number (TAIR)'\n", + "Entity 'http://edamontology.org/data_2781' - Label 'REDIdb ID'\n", + "Entity 'http://edamontology.org/data_2783' - Label 'Protein family ID (PANTHER)'\n", + "Entity 'http://edamontology.org/data_2784' - Label 'RNAVirusDB ID'\n", + "Entity 'http://edamontology.org/data_2786' - Label 'NCBI Genome Project ID'\n", + "Entity 'http://edamontology.org/data_2787' - Label 'NCBI genome accession'\n", + "Entity 'http://edamontology.org/data_2789' - Label 'Protein ID (TopDB)'\n", + "Entity 'http://edamontology.org/data_2792' - Label 'Protein ID (PeroxiBase)'\n", + "Entity 'http://edamontology.org/data_2793' - Label 'SISYPHUS ID'\n", + "Entity 'http://edamontology.org/data_2794' - Label 'ORF ID'\n", + "Entity 'http://edamontology.org/data_2797' - Label 'Protein ID (LGICdb)'\n", + "Entity 'http://edamontology.org/data_2798' - Label 'MaizeDB ID'\n", + "Entity 'http://edamontology.org/data_2799' - Label 'Gene ID (MfunGD)'\n", + "Entity 'http://edamontology.org/data_2800' - Label 'Orpha number'\n", + "Entity 'http://edamontology.org/data_2802' - Label 'Protein ID (EcID)'\n", + "Entity 'http://edamontology.org/data_2803' - Label 'Clone ID (RefSeq)'\n", + "Entity 'http://edamontology.org/data_2804' - Label 'Protein ID (ConoServer)'\n", + "Entity 'http://edamontology.org/data_2805' - Label 'GeneSNP ID'\n", + "Entity 'http://edamontology.org/data_2835' - Label 'Gene ID (VBASE2)'\n", + "Entity 'http://edamontology.org/data_2836' - Label 'DPVweb ID'\n", + "Entity 'http://edamontology.org/data_2915' - Label 'Gramene identifier'\n", + "Entity 'http://edamontology.org/data_2916' - Label 'DDBJ accession'\n", + "Entity 'http://edamontology.org/data_3029' - Label 'Protein ID (EMBL/GenBank/DDBJ)'\n", + "Entity 'http://edamontology.org/data_3103' - Label 'ATC code'\n", + "Entity 'http://edamontology.org/data_3264' - Label 'COSMIC ID'\n", + "Entity 'http://edamontology.org/data_3265' - Label 'HGMD ID'\n", + "Entity 'http://edamontology.org/data_3270' - Label 'Ensembl gene tree ID'\n", + "Entity 'http://edamontology.org/data_3274' - Label 'MGI accession'\n", + "Entity 'http://edamontology.org/data_3757' - Label 'Unimod ID'\n", + "Entity 'http://edamontology.org/data_3769' - Label 'BRENDA ontology concept ID'\n", + "Entity 'http://edamontology.org/data_3856' - Label 'RNA central ID'\n" + ] + } + ], + "source": [ + "query=\"\"\"\n", + "PREFIX edam:\n", + "\n", + "SELECT ?entity ?label ?property WHERE\n", + "{\n", + " ?entity rdfs:subClassOf+ edam:data_2091 .\n", + " ?entity rdfs:label ?label .\n", + " VALUES ?property { edam:regex \n", + " }\n", + " FILTER NOT EXISTS {?entity ?property ?value .}\n", + " \n", + "}ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:30:45.202465Z", + "start_time": "2024-02-13T17:30:45.093914Z" + } + }, + "execution_count": 35 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "PREFIX edam: \n", + "\n", + "CONSTRUCT { \n", + " ?children_format rdfs:subClassOf ?restriction . \n", + " ?restriction rdf:type owl:Restriction ; \n", + " owl:onProperty edam:is_format_of ; \n", + " owl:someValuesFrom ?data. \n", + "}\n", + "WHERE {\n", + " ?parent_format rdfs:subClassOf ?restriction . \n", + " ?restriction rdf:type owl:Restriction ; \n", + " owl:onProperty edam:is_format_of ; \n", + " owl:someValuesFrom ?data.\n", + " ?children_format rdfs:subClassOf+ ?parent_format .\n", + " }\n", + "\"\"\"\n", + "\n", + "#results = kg.query(query)\n", + "\n", + "#for r in results :\n", + "# print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:31:55.773119Z", + "start_time": "2024-02-13T17:31:55.728822Z" + } + }, + "execution_count": 39 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Entity 'http://edamontology.org/data_0849' - Label 'Sequence record'\n", + "Entity 'http://edamontology.org/data_0863' - Label 'Sequence alignment'\n", + "Entity 'http://edamontology.org/data_0863' - Label 'Sequence alignment'\n", + "Entity 'http://edamontology.org/data_0871' - Label 'Phylogenetic character data'\n", + "Entity 'http://edamontology.org/data_0872' - Label 'Phylogenetic tree'\n", + "Entity 'http://edamontology.org/data_0872' - Label 'Phylogenetic tree'\n", + "Entity 'http://edamontology.org/data_0883' - Label 'Structure'\n", + "Entity 'http://edamontology.org/data_1255' - Label 'Sequence features'\n", + "Entity 'http://edamontology.org/data_1354' - Label 'Sequence profile'\n", + "Entity 'http://edamontology.org/data_1381' - Label 'Pair sequence alignment'\n", + "Entity 'http://edamontology.org/data_2044' - Label 'Sequence'\n", + "Entity 'http://edamontology.org/data_2044' - Label 'Sequence'\n", + "Entity 'http://edamontology.org/data_2048' - Label 'Report'\n", + "Entity 'http://edamontology.org/data_2091' - Label 'Accession'\n", + "Entity 'http://edamontology.org/data_2091' - Label 'Accession'\n", + "Entity 'http://edamontology.org/data_2098' - Label 'Job identifier'\n", + "Entity 'http://edamontology.org/data_2099' - Label 'Name'\n", + "Entity 'http://edamontology.org/data_2099' - Label 'Name'\n", + "Entity 'http://edamontology.org/data_2099' - Label 'Name'\n", + "Entity 'http://edamontology.org/data_2100' - Label 'Type'\n", + "Entity 'http://edamontology.org/data_2968' - Label 'Image'\n", + "Entity 'http://edamontology.org/data_2968' - Label 'Image'\n", + "Entity 'http://edamontology.org/data_2976' - Label 'Protein sequence'\n", + "Entity 'http://edamontology.org/data_2977' - Label 'Nucleic acid sequence'\n", + "Entity 'http://edamontology.org/data_3424' - Label 'Raw image'\n", + "Entity 'http://edamontology.org/format_1207' - Label 'nucleotide'\n", + "Entity 'http://edamontology.org/format_1208' - Label 'protein'\n", + "Entity 'http://edamontology.org/format_1212' - Label 'dna'\n", + "Entity 'http://edamontology.org/format_1213' - Label 'rna'\n", + "Entity 'http://edamontology.org/format_1997' - Label 'PHYLIP format'\n", + "Entity 'http://edamontology.org/format_1998' - Label 'PHYLIP sequential'\n", + "Entity 'http://edamontology.org/format_2183' - Label 'EMBLXML'\n", + "Entity 'http://edamontology.org/format_2184' - Label 'cdsxml'\n", + "Entity 'http://edamontology.org/format_2200' - Label 'FASTA-like (text)'\n", + "Entity 'http://edamontology.org/format_2330' - Label 'Textual format'\n", + "Entity 'http://edamontology.org/format_2330' - Label 'Textual format'\n", + "Entity 'http://edamontology.org/format_2330' - Label 'Textual format'\n", + "Entity 'http://edamontology.org/format_2331' - Label 'HTML'\n", + "Entity 'http://edamontology.org/format_2352' - Label 'BioXSD (XML)'\n", + "Entity 'http://edamontology.org/format_2571' - Label 'Raw sequence format'\n", + "Entity 'http://edamontology.org/format_3261' - Label 'RDF/XML'\n", + "Entity 'http://edamontology.org/format_3462' - Label 'CRAM'\n", + "Entity 'http://edamontology.org/format_3484' - Label 'ebwt'\n", + "Entity 'http://edamontology.org/format_3485' - Label 'RSF'\n", + "Entity 'http://edamontology.org/format_3487' - Label 'BSML'\n", + "Entity 'http://edamontology.org/format_3491' - Label 'ebwtl'\n", + "Entity 'http://edamontology.org/format_3607' - Label 'qual'\n", + "Entity 'http://edamontology.org/format_3609' - Label 'qualillumina'\n", + "Entity 'http://edamontology.org/format_3610' - Label 'qualsolid'\n", + "Entity 'http://edamontology.org/format_3611' - Label 'qual454'\n", + "Entity 'http://edamontology.org/format_3654' - Label 'mzXML'\n", + "Entity 'http://edamontology.org/format_3655' - Label 'pepXML'\n", + "Entity 'http://edamontology.org/format_3747' - Label 'protXML'\n", + "Entity 'http://edamontology.org/format_3747' - Label 'protXML'\n", + "Entity 'http://edamontology.org/format_3764' - Label 'idXML'\n", + "Entity 'http://edamontology.org/format_3764' - Label 'idXML'\n", + "Entity 'http://edamontology.org/format_3832' - Label 'consensusXML'\n", + "Entity 'http://edamontology.org/format_3833' - Label 'featureXML'\n", + "Entity 'http://edamontology.org/format_3834' - Label 'mzData'\n", + "Entity 'http://edamontology.org/format_3835' - Label 'TIDE TXT'\n", + "Entity 'http://edamontology.org/format_3836' - Label 'BLAST XML v2 results format'\n", + "Entity 'http://edamontology.org/format_3836' - Label 'BLAST XML v2 results format'\n", + "Entity 'http://edamontology.org/format_3836' - Label 'BLAST XML v2 results format'\n", + "Entity 'http://edamontology.org/format_3982' - Label 'CHAIN'\n", + "Entity 'http://edamontology.org/format_3983' - Label 'NET'\n", + "Entity 'http://edamontology.org/format_3985' - Label 'gxformat2'\n", + "Entity 'http://edamontology.org/format_3992' - Label 'CIGAR format'\n", + "Entity 'http://edamontology.org/format_4000' - Label 'R markdown'\n", + "Entity 'http://edamontology.org/format_4002' - Label 'pickle'\n", + "Entity 'http://edamontology.org/format_4004' - Label 'SimTools repertoire file format'\n", + "Entity 'http://edamontology.org/format_4006' - Label 'Zstandard format'\n", + "Entity 'http://edamontology.org/operation_0558' - Label 'Phylogenetic tree annotation'\n", + "Entity 'http://edamontology.org/topic_0077' - Label 'Nucleic acids'\n", + "Entity 'http://edamontology.org/topic_0077' - Label 'Nucleic acids'\n", + "Entity 'http://edamontology.org/topic_0078' - Label 'Proteins'\n", + "Entity 'http://edamontology.org/topic_0080' - Label 'Sequence analysis'\n", + "Entity 'http://edamontology.org/topic_0081' - Label 'Structure analysis'\n", + "Entity 'http://edamontology.org/topic_0084' - Label 'Phylogeny'\n", + "Entity 'http://edamontology.org/topic_0089' - Label 'Ontology and terminology'\n", + "Entity 'http://edamontology.org/topic_0091' - Label 'Bioinformatics'\n", + "Entity 'http://edamontology.org/topic_0121' - Label 'Proteomics'\n", + "Entity 'http://edamontology.org/topic_0199' - Label 'Genetic variation'\n", + "Entity 'http://edamontology.org/topic_0200' - Label 'Microarrays'\n", + "Entity 'http://edamontology.org/topic_0203' - Label 'Gene expression'\n", + "Entity 'http://edamontology.org/topic_0610' - Label 'Ecology'\n", + "Entity 'http://edamontology.org/topic_0622' - Label 'Genomics'\n", + "Entity 'http://edamontology.org/topic_0632' - Label 'Probes and primers'\n", + "Entity 'http://edamontology.org/topic_0804' - Label 'Immunology'\n", + "Entity 'http://edamontology.org/topic_0804' - Label 'Immunology'\n", + "Entity 'http://edamontology.org/topic_2259' - Label 'Systems biology'\n", + "Entity 'http://edamontology.org/topic_2269' - Label 'Statistics and probability'\n", + "Entity 'http://edamontology.org/topic_2829' - Label 'Ontologies, nomenclature and classification'\n", + "Entity 'http://edamontology.org/topic_3050' - Label 'Biodiversity'\n", + "Entity 'http://edamontology.org/topic_3053' - Label 'Genetics'\n", + "Entity 'http://edamontology.org/topic_3068' - Label 'Literature and language'\n", + "Entity 'http://edamontology.org/topic_3071' - Label 'Data management'\n", + "Entity 'http://edamontology.org/topic_3072' - Label 'Sequence feature detection'\n", + "Entity 'http://edamontology.org/topic_3168' - Label 'Sequencing'\n", + "Entity 'http://edamontology.org/topic_3172' - Label 'Metabolomics'\n", + "Entity 'http://edamontology.org/topic_3173' - Label 'Epigenomics'\n", + "Entity 'http://edamontology.org/topic_3176' - Label 'DNA packaging'\n", + "Entity 'http://edamontology.org/topic_3293' - Label 'Phylogenetics'\n", + "Entity 'http://edamontology.org/topic_3295' - Label 'Epigenetics'\n", + "Entity 'http://edamontology.org/topic_3412' - Label 'Hepatic and biliary medicine'\n", + "Entity 'http://edamontology.org/topic_3571' - Label 'Data governance'\n", + "Entity 'http://edamontology.org/topic_3974' - Label 'Epistasis'\n" + ] + } + ], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?property ?label ?value WHERE {\n", + " VALUES ?property {\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "\n", + "\n", + "}\n", + "\n", + "?entity ?property ?value .\n", + "\n", + "FILTER isLiteral(?value) \n", + "?entity rdfs:label ?label .\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:32:43.406278Z", + "start_time": "2024-02-13T17:32:42.503590Z" + } + }, + "execution_count": 40 + }, + { + "cell_type": "code", + "outputs": [ + { + "ename": "KeyboardInterrupt", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", + "\u001B[0;31mKeyboardInterrupt\u001B[0m Traceback (most recent call last)", + "Cell \u001B[0;32mIn[42], line 37\u001B[0m\n\u001B[1;32m 1\u001B[0m query\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[1;32m 2\u001B[0m \u001B[38;5;124mPREFIX edam:\u001B[39m\n\u001B[1;32m 3\u001B[0m \n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 32\u001B[0m \u001B[38;5;124mORDER BY ?entity\u001B[39m\n\u001B[1;32m 33\u001B[0m \u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[1;32m 35\u001B[0m results \u001B[38;5;241m=\u001B[39m kg\u001B[38;5;241m.\u001B[39mquery(query)\n\u001B[0;32m---> 37\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m r \u001B[38;5;129;01min\u001B[39;00m results :\n\u001B[1;32m 38\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mEntity \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mentity\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m - Label \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mlabel\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m\"\u001B[39m) \n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/query.py:373\u001B[0m, in \u001B[0;36mResult.__iter__\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 369\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mtype \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mSELECT\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 370\u001B[0m \u001B[38;5;66;03m# this iterates over ResultRows of variable bindings\u001B[39;00m\n\u001B[1;32m 372\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_genbindings:\n\u001B[0;32m--> 373\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m b \u001B[38;5;129;01min\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_genbindings:\n\u001B[1;32m 374\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m b: \u001B[38;5;66;03m# don't add a result row in case of empty binding {}\u001B[39;00m\n\u001B[1;32m 375\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_bindings\u001B[38;5;241m.\u001B[39mappend(b)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:551\u001B[0m, in \u001B[0;36mevalDistinct\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 548\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mevalDistinct\u001B[39m(\n\u001B[1;32m 549\u001B[0m ctx: QueryContext, part: CompValue\n\u001B[1;32m 550\u001B[0m ) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m Generator[FrozenBindings, \u001B[38;5;28;01mNone\u001B[39;00m, \u001B[38;5;28;01mNone\u001B[39;00m]:\n\u001B[0;32m--> 551\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mp\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 553\u001B[0m done \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mset\u001B[39m()\n\u001B[1;32m 554\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m x \u001B[38;5;129;01min\u001B[39;00m res:\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:303\u001B[0m, in \u001B[0;36mevalPart\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 300\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalMinus(ctx, part)\n\u001B[1;32m 302\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mProject\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m--> 303\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mevalProject\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 304\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mSlice\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 305\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalSlice(ctx, part)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:561\u001B[0m, in \u001B[0;36mevalProject\u001B[0;34m(ctx, project)\u001B[0m\n\u001B[1;32m 560\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mevalProject\u001B[39m(ctx: QueryContext, project: CompValue):\n\u001B[0;32m--> 561\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mproject\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mp\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 562\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m (row\u001B[38;5;241m.\u001B[39mproject(project\u001B[38;5;241m.\u001B[39mPV) \u001B[38;5;28;01mfor\u001B[39;00m row \u001B[38;5;129;01min\u001B[39;00m res)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:312\u001B[0m, in \u001B[0;36mevalPart\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 309\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalReduced(ctx, part)\n\u001B[1;32m 311\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mOrderBy\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m--> 312\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mevalOrderBy\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 313\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mGroup\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 314\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalGroup(ctx, part)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:491\u001B[0m, in \u001B[0;36mevalOrderBy\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 489\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m e \u001B[38;5;129;01min\u001B[39;00m \u001B[38;5;28mreversed\u001B[39m(part\u001B[38;5;241m.\u001B[39mexpr):\n\u001B[1;32m 490\u001B[0m reverse \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mbool\u001B[39m(e\u001B[38;5;241m.\u001B[39morder \u001B[38;5;129;01mand\u001B[39;00m e\u001B[38;5;241m.\u001B[39morder \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mDESC\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[0;32m--> 491\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43msorted\u001B[39;49m\u001B[43m(\u001B[49m\n\u001B[1;32m 492\u001B[0m \u001B[43m \u001B[49m\u001B[43mres\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mkey\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mlambda\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mx\u001B[49m\u001B[43m:\u001B[49m\u001B[43m \u001B[49m\u001B[43m_val\u001B[49m\u001B[43m(\u001B[49m\u001B[43mvalue\u001B[49m\u001B[43m(\u001B[49m\u001B[43mx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43me\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mexpr\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mvariables\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mTrue\u001B[39;49;00m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mreverse\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mreverse\u001B[49m\n\u001B[1;32m 493\u001B[0m \u001B[43m \u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 495\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m res\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:205\u001B[0m, in \u001B[0;36mevalFilter\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 200\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mevalFilter\u001B[39m(\n\u001B[1;32m 201\u001B[0m ctx: QueryContext, part: CompValue\n\u001B[1;32m 202\u001B[0m ) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m Generator[FrozenBindings, \u001B[38;5;28;01mNone\u001B[39;00m, \u001B[38;5;28;01mNone\u001B[39;00m]:\n\u001B[1;32m 203\u001B[0m \u001B[38;5;66;03m# TODO: Deal with dict returned from evalPart!\u001B[39;00m\n\u001B[1;32m 204\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m c \u001B[38;5;129;01min\u001B[39;00m evalPart(ctx, part\u001B[38;5;241m.\u001B[39mp):\n\u001B[0;32m--> 205\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[43m_ebv\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 206\u001B[0m \u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mexpr\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 207\u001B[0m \u001B[43m \u001B[49m\u001B[43mc\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mforget\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43m_except\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mpart\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_vars\u001B[49m\u001B[43m)\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;28;43;01mif\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[38;5;129;43;01mnot\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mno_isolated_scope\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;28;43;01melse\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[43mc\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 208\u001B[0m \u001B[43m \u001B[49m\u001B[43m)\u001B[49m:\n\u001B[1;32m 209\u001B[0m \u001B[38;5;28;01myield\u001B[39;00m c\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evalutils.py:90\u001B[0m, in \u001B[0;36m_ebv\u001B[0;34m(expr, ctx)\u001B[0m\n\u001B[1;32m 88\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(expr, Expr):\n\u001B[1;32m 89\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m---> 90\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m EBV(\u001B[43mexpr\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43meval\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m)\u001B[49m)\n\u001B[1;32m 91\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m SPARQLError:\n\u001B[1;32m 92\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;01mFalse\u001B[39;00m \u001B[38;5;66;03m# filter error == False\u001B[39;00m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parserutils.py:228\u001B[0m, in \u001B[0;36mExpr.eval\u001B[0;34m(self, ctx)\u001B[0m\n\u001B[1;32m 226\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mctx: Optional[Union[Mapping, FrozenBindings]] \u001B[38;5;241m=\u001B[39m ctx\n\u001B[1;32m 227\u001B[0m \u001B[38;5;66;03m# type error: \"None\" not callable\u001B[39;00m\n\u001B[0;32m--> 228\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_evalfn\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m)\u001B[49m \u001B[38;5;66;03m# type: ignore[misc]\u001B[39;00m\n\u001B[1;32m 229\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m SPARQLError \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m 230\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m e\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/operators.py:929\u001B[0m, in \u001B[0;36mConditionalAndExpression\u001B[0;34m(e, ctx)\u001B[0m\n\u001B[1;32m 923\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mConditionalAndExpression\u001B[39m(\n\u001B[1;32m 924\u001B[0m e: Expr, ctx: Union[QueryContext, FrozenBindings]\n\u001B[1;32m 925\u001B[0m ) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m Literal:\n\u001B[1;32m 926\u001B[0m \u001B[38;5;66;03m# TODO: handle returned errors\u001B[39;00m\n\u001B[1;32m 928\u001B[0m expr \u001B[38;5;241m=\u001B[39m e\u001B[38;5;241m.\u001B[39mexpr\n\u001B[0;32m--> 929\u001B[0m other \u001B[38;5;241m=\u001B[39m \u001B[43me\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mother\u001B[49m\n\u001B[1;32m 931\u001B[0m \u001B[38;5;66;03m# because of the way the add-expr production handled operator precedence\u001B[39;00m\n\u001B[1;32m 932\u001B[0m \u001B[38;5;66;03m# we sometimes have nothing to do\u001B[39;00m\n\u001B[1;32m 933\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m other \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m:\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parserutils.py:196\u001B[0m, in \u001B[0;36mCompValue.__getattr__\u001B[0;34m(self, a)\u001B[0m\n\u001B[1;32m 194\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mAttributeError\u001B[39;00m()\n\u001B[1;32m 195\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 196\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[43m[\u001B[49m\u001B[43ma\u001B[49m\u001B[43m]\u001B[49m\n\u001B[1;32m 197\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mKeyError\u001B[39;00m:\n\u001B[1;32m 198\u001B[0m \u001B[38;5;66;03m# raise AttributeError('no such attribute '+a)\u001B[39;00m\n\u001B[1;32m 199\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parserutils.py:184\u001B[0m, in \u001B[0;36mCompValue.__getitem__\u001B[0;34m(self, a)\u001B[0m\n\u001B[1;32m 183\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21m__getitem__\u001B[39m(\u001B[38;5;28mself\u001B[39m, a):\n\u001B[0;32m--> 184\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_value\u001B[49m\u001B[43m(\u001B[49m\u001B[43mOrderedDict\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[38;5;21;43m__getitem__\u001B[39;49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43ma\u001B[49m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parserutils.py:179\u001B[0m, in \u001B[0;36mCompValue._value\u001B[0;34m(self, val, variables, errors)\u001B[0m\n\u001B[1;32m 175\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21m_value\u001B[39m(\n\u001B[1;32m 176\u001B[0m \u001B[38;5;28mself\u001B[39m, val: _ValT, variables: \u001B[38;5;28mbool\u001B[39m \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;01mFalse\u001B[39;00m, errors: \u001B[38;5;28mbool\u001B[39m \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;01mFalse\u001B[39;00m\n\u001B[1;32m 177\u001B[0m ) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m Union[_ValT, Any]:\n\u001B[1;32m 178\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mctx \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m:\n\u001B[0;32m--> 179\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mvalue\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mval\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mvariables\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 180\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 181\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m val\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parserutils.py:81\u001B[0m, in \u001B[0;36mvalue\u001B[0;34m(ctx, val, variables, errors)\u001B[0m\n\u001B[1;32m 78\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mException\u001B[39;00m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mWhat do I do with this CompValue? \u001B[39m\u001B[38;5;132;01m%s\u001B[39;00m\u001B[38;5;124m\"\u001B[39m \u001B[38;5;241m%\u001B[39m val)\n\u001B[1;32m 80\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(val, \u001B[38;5;28mlist\u001B[39m):\n\u001B[0;32m---> 81\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m [value(ctx, x, variables, errors) \u001B[38;5;28;01mfor\u001B[39;00m x \u001B[38;5;129;01min\u001B[39;00m val]\n\u001B[1;32m 83\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(val, (BNode, Variable)):\n\u001B[1;32m 84\u001B[0m r \u001B[38;5;241m=\u001B[39m ctx\u001B[38;5;241m.\u001B[39mget(val)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parserutils.py:81\u001B[0m, in \u001B[0;36m\u001B[0;34m(.0)\u001B[0m\n\u001B[1;32m 78\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mException\u001B[39;00m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mWhat do I do with this CompValue? \u001B[39m\u001B[38;5;132;01m%s\u001B[39;00m\u001B[38;5;124m\"\u001B[39m \u001B[38;5;241m%\u001B[39m val)\n\u001B[1;32m 80\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(val, \u001B[38;5;28mlist\u001B[39m):\n\u001B[0;32m---> 81\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m [\u001B[43mvalue\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mvariables\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43merrors\u001B[49m\u001B[43m)\u001B[49m \u001B[38;5;28;01mfor\u001B[39;00m x \u001B[38;5;129;01min\u001B[39;00m val]\n\u001B[1;32m 83\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(val, (BNode, Variable)):\n\u001B[1;32m 84\u001B[0m r \u001B[38;5;241m=\u001B[39m ctx\u001B[38;5;241m.\u001B[39mget(val)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parserutils.py:76\u001B[0m, in \u001B[0;36mvalue\u001B[0;34m(ctx, val, variables, errors)\u001B[0m\n\u001B[1;32m 63\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 64\u001B[0m \u001B[38;5;124;03mutility function for evaluating something...\u001B[39;00m\n\u001B[1;32m 65\u001B[0m \n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 72\u001B[0m \n\u001B[1;32m 73\u001B[0m \u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 75\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(val, Expr):\n\u001B[0;32m---> 76\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mval\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43meval\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m)\u001B[49m \u001B[38;5;66;03m# recurse?\u001B[39;00m\n\u001B[1;32m 77\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(val, CompValue):\n\u001B[1;32m 78\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mException\u001B[39;00m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mWhat do I do with this CompValue? \u001B[39m\u001B[38;5;132;01m%s\u001B[39;00m\u001B[38;5;124m\"\u001B[39m \u001B[38;5;241m%\u001B[39m val)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parserutils.py:228\u001B[0m, in \u001B[0;36mExpr.eval\u001B[0;34m(self, ctx)\u001B[0m\n\u001B[1;32m 226\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mctx: Optional[Union[Mapping, FrozenBindings]] \u001B[38;5;241m=\u001B[39m ctx\n\u001B[1;32m 227\u001B[0m \u001B[38;5;66;03m# type error: \"None\" not callable\u001B[39;00m\n\u001B[0;32m--> 228\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_evalfn\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m)\u001B[49m \u001B[38;5;66;03m# type: ignore[misc]\u001B[39;00m\n\u001B[1;32m 229\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m SPARQLError \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m 230\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m e\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/operators.py:583\u001B[0m, in \u001B[0;36mBuiltin_EXISTS\u001B[0;34m(e, ctx)\u001B[0m\n\u001B[1;32m 581\u001B[0m ctx \u001B[38;5;241m=\u001B[39m ctx\u001B[38;5;241m.\u001B[39mctx\u001B[38;5;241m.\u001B[39mthaw(ctx) \u001B[38;5;66;03m# type: ignore[assignment] # hmm\u001B[39;00m\n\u001B[1;32m 582\u001B[0m \u001B[38;5;66;03m# type error: Argument 1 to \"evalPart\" has incompatible type \"FrozenBindings\"; expected \"QueryContext\"\u001B[39;00m\n\u001B[0;32m--> 583\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m x \u001B[38;5;129;01min\u001B[39;00m \u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43me\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mgraph\u001B[49m\u001B[43m)\u001B[49m: \u001B[38;5;66;03m# type: ignore[arg-type]\u001B[39;00m\n\u001B[1;32m 584\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m Literal(exists)\n\u001B[1;32m 585\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m Literal(\u001B[38;5;129;01mnot\u001B[39;00m exists)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:300\u001B[0m, in \u001B[0;36mevalPart\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 298\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalExtend(ctx, part)\n\u001B[1;32m 299\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mMinus\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m--> 300\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mevalMinus\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 302\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mProject\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 303\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalProject(ctx, part)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:171\u001B[0m, in \u001B[0;36mevalMinus\u001B[0;34m(ctx, minus)\u001B[0m\n\u001B[1;32m 169\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mevalMinus\u001B[39m(ctx: QueryContext, minus: CompValue) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m Generator[FrozenDict, \u001B[38;5;28;01mNone\u001B[39;00m, \u001B[38;5;28;01mNone\u001B[39;00m]:\n\u001B[1;32m 170\u001B[0m a \u001B[38;5;241m=\u001B[39m evalPart(ctx, minus\u001B[38;5;241m.\u001B[39mp1)\n\u001B[0;32m--> 171\u001B[0m b \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mset\u001B[39m(\u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mminus\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mp2\u001B[49m\u001B[43m)\u001B[49m)\n\u001B[1;32m 172\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m _minus(a, b)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:288\u001B[0m, in \u001B[0;36mevalPart\u001B[0;34m(ctx, part)\u001B[0m\n\u001B[1;32m 286\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalFilter(ctx, part)\n\u001B[1;32m 287\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mJoin\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m--> 288\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mevalJoin\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mpart\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 289\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m part\u001B[38;5;241m.\u001B[39mname \u001B[38;5;241m==\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mLeftJoin\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 290\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalLeftJoin(ctx, part)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:156\u001B[0m, in \u001B[0;36mevalJoin\u001B[0;34m(ctx, join)\u001B[0m\n\u001B[1;32m 154\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 155\u001B[0m a \u001B[38;5;241m=\u001B[39m evalPart(ctx, join\u001B[38;5;241m.\u001B[39mp1)\n\u001B[0;32m--> 156\u001B[0m b \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mset\u001B[39;49m\u001B[43m(\u001B[49m\u001B[43mevalPart\u001B[49m\u001B[43m(\u001B[49m\u001B[43mctx\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mjoin\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mp2\u001B[49m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 157\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m _join(a, b)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/evaluate.py:90\u001B[0m, in \u001B[0;36mevalBGP\u001B[0;34m(ctx, bgp)\u001B[0m\n\u001B[1;32m 88\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m ss, sp, so \u001B[38;5;129;01min\u001B[39;00m ctx\u001B[38;5;241m.\u001B[39mgraph\u001B[38;5;241m.\u001B[39mtriples((_s, _p, _o)): \u001B[38;5;66;03m# type: ignore[union-attr, arg-type]\u001B[39;00m\n\u001B[1;32m 89\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01min\u001B[39;00m (_s, _p, _o):\n\u001B[0;32m---> 90\u001B[0m c \u001B[38;5;241m=\u001B[39m \u001B[43mctx\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mpush\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 91\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 92\u001B[0m c \u001B[38;5;241m=\u001B[39m ctx\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/sparql.py:396\u001B[0m, in \u001B[0;36mQueryContext.push\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 395\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mpush\u001B[39m(\u001B[38;5;28mself\u001B[39m) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mQueryContext\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[0;32m--> 396\u001B[0m r \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mclone\u001B[49m\u001B[43m(\u001B[49m\u001B[43mBindings\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mbindings\u001B[49m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 397\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m r\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/sparql.py:295\u001B[0m, in \u001B[0;36mQueryContext.clone\u001B[0;34m(self, bindings)\u001B[0m\n\u001B[1;32m 290\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mclone\u001B[39m(\n\u001B[1;32m 291\u001B[0m \u001B[38;5;28mself\u001B[39m, bindings: Optional[Union[FrozenBindings, Bindings, List[Any]]] \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;01mNone\u001B[39;00m\n\u001B[1;32m 292\u001B[0m ) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mQueryContext\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 293\u001B[0m r \u001B[38;5;241m=\u001B[39m QueryContext(\n\u001B[1;32m 294\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_dataset \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_dataset \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;28;01melse\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mgraph,\n\u001B[0;32m--> 295\u001B[0m bindings \u001B[38;5;129;01mor\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mbindings,\n\u001B[1;32m 296\u001B[0m initBindings\u001B[38;5;241m=\u001B[39m\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39minitBindings,\n\u001B[1;32m 297\u001B[0m )\n\u001B[1;32m 298\u001B[0m r\u001B[38;5;241m.\u001B[39mprologue \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mprologue\n\u001B[1;32m 299\u001B[0m r\u001B[38;5;241m.\u001B[39mgraph \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mgraph\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/sparql.py:98\u001B[0m, in \u001B[0;36mBindings.__len__\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 96\u001B[0m i \u001B[38;5;241m=\u001B[39m \u001B[38;5;241m0\u001B[39m\n\u001B[1;32m 97\u001B[0m d: Optional[Bindings] \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\n\u001B[0;32m---> 98\u001B[0m \u001B[38;5;28;01mwhile\u001B[39;00m d \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m:\n\u001B[1;32m 99\u001B[0m i \u001B[38;5;241m+\u001B[39m\u001B[38;5;241m=\u001B[39m \u001B[38;5;28mlen\u001B[39m(d\u001B[38;5;241m.\u001B[39m_d)\n\u001B[1;32m 100\u001B[0m d \u001B[38;5;241m=\u001B[39m d\u001B[38;5;241m.\u001B[39mouter\n", + "\u001B[0;31mKeyboardInterrupt\u001B[0m: " + ] + } + ], + "source": [ + "query=\"\"\"\n", + "PREFIX edam:\n", + "\n", + "SELECT DISTINCT ?entity ?property ?label ?property_subs_edam WHERE {\n", + "\n", + " VALUES ?property {oboInOwl:hasDefinition\n", + " edam:created_in\n", + " #oboInOwl:inSubset\n", + " rdfs:label\n", + " rdfs:subClassOf }\n", + " ?entity a owl:Class .\n", + "\n", + " FILTER NOT EXISTS {?entity owl:deprecated true .}\n", + " OPTIONAL {?entity rdfs:label ?label .}\n", + " FILTER ( ?entity != )\n", + " FILTER ( ?entity != )\n", + " FILTER ( ?entity != )\n", + " FILTER ( ?entity != )\n", + " FILTER ( ?entity != )\n", + "\n", + " FILTER NOT EXISTS {?entity ?property ?value .\n", + " MINUS { ?value rdf:type owl:Restriction .} #to prevent concept with rdfs:subClassOf property being only restriction (e.g. has_topic)\n", + " }\n", + " FILTER (!isBlank(?entity))\n", + " # UNION\n", + " # {\n", + " # VALUES ?property { oboInOwl:inSubset\n", + " # }\n", + " # FILTER NOT EXISTS {?entity ?property .}\n", + " # }\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:34:51.916015Z", + "start_time": "2024-02-13T17:33:28.687288Z" + } + }, + "execution_count": 42 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "PREFIX edam:\n", + "\n", + "SELECT DISTINCT ?entity ?property ?label WHERE {\n", + " \n", + " ?entity owl:deprecated true .\n", + " ?entity rdfs:label ?label .\n", + " FILTER ( ?entity != )\n", + " \n", + " {VALUES ?property { edam:obsolete_since\n", + " edam:oldParent \n", + " }\n", + " FILTER NOT EXISTS {?entity ?property ?value .}\n", + " }\n", + " # UNION\n", + " # {VALUES ?property { oboInOwl:inSubset \n", + " # }\n", + " # FILTER NOT EXISTS {?entity ?property .}\n", + " # }\n", + " UNION\n", + " {VALUES ?property { rdfs:subClassOf \n", + " }\n", + " FILTER NOT EXISTS {?entity ?property .}}\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:35:44.305467Z", + "start_time": "2024-02-13T17:35:44.131381Z" + } + }, + "execution_count": 44 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "PREFIX edam:\n", + "PREFIX xsd: \n", + "\n", + "SELECT DISTINCT ?entity ?target ?label ?property\n", + "WHERE {\n", + " VALUES ?property { edam:has_topic\n", + " edam:has_input\n", + " edam:has_output\n", + " edam:is_format_of\n", + " edam:is_identifier_of\n", + " \n", + " }\n", + " ?entity ?p ?value .\n", + " #{?entity rdfs:subClassOf+ edam:operation_0004 .}\n", + " #UNION\n", + " #{\n", + " #?entity rdfs:subClassOf+ edam:data_0006 .\n", + " #}\n", + " ?entity rdfs:label ?label .\n", + " ?entity rdfs:subClassOf ?restriction . \n", + " ?restriction rdf:type owl:Restriction ; \n", + " owl:onProperty ?property ; \n", + " owl:someValuesFrom ?target.\n", + " ?target owl:deprecated ?deprecated . \n", + " FILTER (?deprecated = true)\n", + "}\n", + "ORDER BY ?entity \n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:36:22.365946Z", + "start_time": "2024-02-13T17:36:22.359500Z" + } + }, + "execution_count": 45 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "PREFIX edam:\n", + "PREFIX xsd: \n", + "\n", + "SELECT DISTINCT ?entity ?label ?value ?property WHERE {\n", + " \n", + " ?entity rdfs:subClassOf ?restriction . \n", + " ?restriction rdf:type owl:Restriction ;\n", + " owl:onProperty ?property ; \n", + " owl:someValuesFrom ?value .\n", + " ?value edam:notRecommendedForAnnotation true .\n", + " \n", + " FILTER ( ?entity != )\n", + " FILTER ( ?entity != )\n", + " FILTER ( ?entity != )\n", + " ?entity rdfs:label ?label .\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:36:58.570387Z", + "start_time": "2024-02-13T17:36:57.590318Z" + } + }, + "execution_count": 46 + }, + { + "cell_type": "code", + "outputs": [ + { + "ename": "ParseException", + "evalue": "Expected SelectQuery, found 'FILTER' (at char 169), (line:7, col:4)", + "output_type": "error", + "traceback": [ + "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", + "\u001B[0;31mParseException\u001B[0m Traceback (most recent call last)", + "Cell \u001B[0;32mIn[48], line 14\u001B[0m\n\u001B[1;32m 1\u001B[0m query\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[1;32m 2\u001B[0m \u001B[38;5;124mPREFIX edam:\u001B[39m\n\u001B[1;32m 3\u001B[0m \n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 11\u001B[0m \u001B[38;5;124mORDER BY ?entity\u001B[39m\n\u001B[1;32m 12\u001B[0m \u001B[38;5;124m\"\"\"\u001B[39m\n\u001B[0;32m---> 14\u001B[0m results \u001B[38;5;241m=\u001B[39m \u001B[43mkg\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mquery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquery\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 16\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m r \u001B[38;5;129;01min\u001B[39;00m results :\n\u001B[1;32m 17\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mEntity \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mentity\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m - Label \u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mr[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mlabel\u001B[39m\u001B[38;5;124m'\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m\"\u001B[39m) \n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/graph.py:1565\u001B[0m, in \u001B[0;36mGraph.query\u001B[0;34m(self, query_object, processor, result, initNs, initBindings, use_store_provided, **kwargs)\u001B[0m\n\u001B[1;32m 1562\u001B[0m processor \u001B[38;5;241m=\u001B[39m plugin\u001B[38;5;241m.\u001B[39mget(processor, query\u001B[38;5;241m.\u001B[39mProcessor)(\u001B[38;5;28mself\u001B[39m)\n\u001B[1;32m 1564\u001B[0m \u001B[38;5;66;03m# type error: Argument 1 to \"Result\" has incompatible type \"Mapping[str, Any]\"; expected \"str\"\u001B[39;00m\n\u001B[0;32m-> 1565\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m result(\u001B[43mprocessor\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mquery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquery_object\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43minitBindings\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43minitNs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/processor.py:144\u001B[0m, in \u001B[0;36mSPARQLProcessor.query\u001B[0;34m(self, strOrQuery, initBindings, initNs, base, DEBUG)\u001B[0m\n\u001B[1;32m 124\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 125\u001B[0m \u001B[38;5;124;03mEvaluate a query with the given initial bindings, and initial\u001B[39;00m\n\u001B[1;32m 126\u001B[0m \u001B[38;5;124;03mnamespaces. The given base is used to resolve relative URIs in\u001B[39;00m\n\u001B[0;32m (...)\u001B[0m\n\u001B[1;32m 140\u001B[0m \u001B[38;5;124;03m documentation.\u001B[39;00m\n\u001B[1;32m 141\u001B[0m \u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[1;32m 143\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(strOrQuery, \u001B[38;5;28mstr\u001B[39m):\n\u001B[0;32m--> 144\u001B[0m strOrQuery \u001B[38;5;241m=\u001B[39m translateQuery(\u001B[43mparseQuery\u001B[49m\u001B[43m(\u001B[49m\u001B[43mstrOrQuery\u001B[49m\u001B[43m)\u001B[49m, base, initNs)\n\u001B[1;32m 146\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m evalQuery(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mgraph, strOrQuery, initBindings, base)\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/rdflib/plugins/sparql/parser.py:1542\u001B[0m, in \u001B[0;36mparseQuery\u001B[0;34m(q)\u001B[0m\n\u001B[1;32m 1539\u001B[0m q \u001B[38;5;241m=\u001B[39m q\u001B[38;5;241m.\u001B[39mdecode(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mutf-8\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 1541\u001B[0m q \u001B[38;5;241m=\u001B[39m expandUnicodeEscapes(q)\n\u001B[0;32m-> 1542\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mQuery\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mparseString\u001B[49m\u001B[43m(\u001B[49m\u001B[43mq\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mparseAll\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mTrue\u001B[39;49;00m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/pyparsing/util.py:256\u001B[0m, in \u001B[0;36m_make_synonym_function.._inner\u001B[0;34m(self, *args, **kwargs)\u001B[0m\n\u001B[1;32m 251\u001B[0m \u001B[38;5;129m@wraps\u001B[39m(fn)\n\u001B[1;32m 252\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21m_inner\u001B[39m(\u001B[38;5;28mself\u001B[39m, \u001B[38;5;241m*\u001B[39margs, \u001B[38;5;241m*\u001B[39m\u001B[38;5;241m*\u001B[39mkwargs):\n\u001B[1;32m 253\u001B[0m \u001B[38;5;66;03m# warnings.warn(\u001B[39;00m\n\u001B[1;32m 254\u001B[0m \u001B[38;5;66;03m# f\"Deprecated - use {fn.__name__}\", DeprecationWarning, stacklevel=3\u001B[39;00m\n\u001B[1;32m 255\u001B[0m \u001B[38;5;66;03m# )\u001B[39;00m\n\u001B[0;32m--> 256\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mfn\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43margs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n", + "File \u001B[0;32m~/mambaforge/lib/python3.10/site-packages/pyparsing/core.py:1197\u001B[0m, in \u001B[0;36mParserElement.parse_string\u001B[0;34m(self, instring, parse_all, parseAll)\u001B[0m\n\u001B[1;32m 1194\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m\n\u001B[1;32m 1195\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1196\u001B[0m \u001B[38;5;66;03m# catch and re-raise exception from here, clearing out pyparsing internal stack trace\u001B[39;00m\n\u001B[0;32m-> 1197\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m exc\u001B[38;5;241m.\u001B[39mwith_traceback(\u001B[38;5;28;01mNone\u001B[39;00m)\n\u001B[1;32m 1198\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 1199\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m tokens\n", + "\u001B[0;31mParseException\u001B[0m: Expected SelectQuery, found 'FILTER' (at char 169), (line:7, col:4)" + ] + } + ], + "source": [ + "query=\"\"\"\n", + "PREFIX edam:\n", + "\n", + "SELECT DISTINCT ?entity ?property ?value ?label WHERE {\n", + " ?entity ?property ?value .\n", + " ?entity rdfs:label ?label . \n", + " FILTER REGEX(str(?value), \"^[\\\\s\\r\\n]+\")\n", + " FILTER (!isBlank(?entity))\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:37:43.255350Z", + "start_time": "2024-02-13T17:37:43.213404Z" + } + }, + "execution_count": 48 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "PREFIX edam:\n", + "PREFIX xsd: \n", + "\n", + "SELECT ?entity ?label ?id ?subset ?superclass ?label_sc ?id_sc ?subset_sc WHERE {\n", + "\n", + " ?entity a owl:Class .\n", + " ?entity rdfs:label ?label . \n", + " BIND(strafter(str(?entity), \"org/\") AS ?id) .\n", + " BIND(strbefore(str(?id), \"_\") AS ?subset) .\n", + " \n", + " ?entity rdfs:subClassOf ?superclass .\n", + " ?superclass rdfs:label ?label_sc . \n", + " BIND(strafter(str(?superclass), \"org/\") AS ?id_sc) .\n", + " BIND(strbefore(str(?id_sc), \"_\") AS ?subset_sc) .\n", + " \n", + " FILTER ( ?subset_sc != ?subset) .\n", + "} \n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:38:31.933779Z", + "start_time": "2024-02-13T17:38:31.263856Z" + } + }, + "execution_count": 49 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?label ?property ?value WHERE {\n", + " VALUES ?property { rdfs:subClassOf }\n", + " ?entity ?property ?value\n", + " FILTER (?entity = ?value)\n", + "\t ?entity rdfs:label ?label \n", + "\t \n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:39:00.957289Z", + "start_time": "2024-02-13T17:39:00.769363Z" + } + }, + "execution_count": 50 + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "query=\"\"\"\n", + "SELECT DISTINCT ?entity ?property ?value ?label WHERE {\n", + " ?entity ?property ?value .\n", + " ?entity rdfs:label ?label . \n", + " \n", + " FILTER regex(?value, \"\\t\")\n", + " FILTER (!isBlank(?entity))\n", + "\n", + "}\n", + "ORDER BY ?entity\n", + "\"\"\"\n", + "\n", + "results = kg.query(query)\n", + "\n", + "for r in results :\n", + " print(f\"Entity '{r['entity']}' - Label '{r['label']}'\") " + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-02-13T17:39:44.609247Z", + "start_time": "2024-02-13T17:39:42.950288Z" + } + }, + "execution_count": 51 + }, + { + "cell_type": "code", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Entity 'http://edamontology.org/data_0005' - Label 'Resource type'\n", + "Entity 'http://edamontology.org/data_0005' - Label 'Resource type'\n", + "Entity 'http://edamontology.org/data_0007' - Label 'Tool'\n", + "Entity 'http://edamontology.org/data_0007' - Label 'Tool'\n", + "Entity 'http://edamontology.org/data_0581' - Label 'Database'\n", + "Entity 'http://edamontology.org/data_0581' - Label 'Database'\n", + "Entity 'http://edamontology.org/data_0582' - Label 'Ontology'\n", + "Entity 'http://edamontology.org/data_0582' - Label 'Ontology'\n", + "Entity 'http://edamontology.org/data_0583' - Label 'Directory metadata'\n", + "Entity 'http://edamontology.org/data_0583' - Label 'Directory metadata'\n", + "Entity 'http://edamontology.org/data_0831' - Label 'MeSH vocabulary'\n", + "Entity 'http://edamontology.org/data_0831' - Label 'MeSH vocabulary'\n", + "Entity 'http://edamontology.org/data_0832' - Label 'HGNC vocabulary'\n", + "Entity 'http://edamontology.org/data_0832' - Label 'HGNC vocabulary'\n", + "Entity 'http://edamontology.org/data_0835' - Label 'UMLS vocabulary'\n", + "Entity 'http://edamontology.org/data_0835' - Label 'UMLS vocabulary'\n", + "Entity 'http://edamontology.org/data_0842' - Label 'Identifier'\n", + "Entity 'http://edamontology.org/data_0842' - Label 'Identifier'\n", + "Entity 'http://edamontology.org/data_0843' - Label 'Database entry'\n", + "Entity 'http://edamontology.org/data_0843' - Label 'Database entry'\n", + "Entity 'http://edamontology.org/data_0844' - Label 'Molecular mass'\n", + "Entity 'http://edamontology.org/data_0845' - Label 'Molecular charge'\n", + "Entity 'http://edamontology.org/data_0846' - Label 'Chemical formula'\n", + "Entity 'http://edamontology.org/data_0847' - Label 'QSAR descriptor'\n", + "Entity 'http://edamontology.org/data_0848' - Label 'Raw sequence'\n", + "Entity 'http://edamontology.org/data_0848' - Label 'Raw sequence'\n", + "Entity 'http://edamontology.org/data_0849' - Label 'Sequence record'\n", + "Entity 'http://edamontology.org/data_0850' - Label 'Sequence set'\n", + "Entity 'http://edamontology.org/data_0851' - Label 'Sequence mask character'\n", + "Entity 'http://edamontology.org/data_0851' - Label 'Sequence mask character'\n", + "Entity 'http://edamontology.org/data_0852' - Label 'Sequence mask type'\n", + "Entity 'http://edamontology.org/data_0852' - Label 'Sequence mask type'\n", + "Entity 'http://edamontology.org/data_0853' - Label 'DNA sense specification'\n", + "Entity 'http://edamontology.org/data_0853' - Label 'DNA sense specification'\n", + "Entity 'http://edamontology.org/data_0854' - Label 'Sequence length specification'\n", + "Entity 'http://edamontology.org/data_0854' - Label 'Sequence length specification'\n", + "Entity 'http://edamontology.org/data_0855' - Label 'Sequence metadata'\n", + "Entity 'http://edamontology.org/data_0855' - Label 'Sequence metadata'\n", + "Entity 'http://edamontology.org/data_0856' - Label 'Sequence feature source'\n", + "Entity 'http://edamontology.org/data_0857' - Label 'Sequence search results'\n", + "Entity 'http://edamontology.org/data_0858' - Label 'Sequence signature matches'\n", + "Entity 'http://edamontology.org/data_0858' - Label 'Sequence signature matches'\n", + "Entity 'http://edamontology.org/data_0859' - Label 'Sequence signature model'\n", + "Entity 'http://edamontology.org/data_0859' - Label 'Sequence signature model'\n", + "Entity 'http://edamontology.org/data_0860' - Label 'Sequence signature data'\n", + "Entity 'http://edamontology.org/data_0860' - Label 'Sequence signature data'\n", + "Entity 'http://edamontology.org/data_0861' - Label 'Sequence alignment (words)'\n", + "Entity 'http://edamontology.org/data_0861' - Label 'Sequence alignment (words)'\n", + "Entity 'http://edamontology.org/data_0862' - Label 'Dotplot'\n", + "Entity 'http://edamontology.org/data_0863' - Label 'Sequence alignment'\n", + "Entity 'http://edamontology.org/data_0863' - Label 'Sequence alignment'\n", + "Entity 'http://edamontology.org/data_0864' - Label 'Sequence alignment parameter'\n", + "Entity 'http://edamontology.org/data_0864' - Label 'Sequence alignment parameter'\n", + "Entity 'http://edamontology.org/data_0865' - Label 'Sequence similarity score'\n", + "Entity 'http://edamontology.org/data_0866' - Label 'Sequence alignment metadata'\n", + "Entity 'http://edamontology.org/data_0866' - Label 'Sequence alignment metadata'\n", + "Entity 'http://edamontology.org/data_0867' - Label 'Sequence alignment report'\n", + "Entity 'http://edamontology.org/data_0868' - Label 'Profile-profile alignment'\n", + "Entity 'http://edamontology.org/data_0868' - Label 'Profile-profile alignment'\n", + "Entity 'http://edamontology.org/data_0869' - Label 'Sequence-profile alignment'\n", + "Entity 'http://edamontology.org/data_0869' - Label 'Sequence-profile alignment'\n", + "Entity 'http://edamontology.org/data_0870' - Label 'Sequence distance matrix'\n", + "Entity 'http://edamontology.org/data_0871' - Label 'Phylogenetic character data'\n", + "Entity 'http://edamontology.org/data_0872' - Label 'Phylogenetic tree'\n", + "Entity 'http://edamontology.org/data_0872' - Label 'Phylogenetic tree'\n", + "Entity 'http://edamontology.org/data_0874' - Label 'Comparison matrix'\n", + "Entity 'http://edamontology.org/data_0875' - Label 'Protein topology'\n", + "Entity 'http://edamontology.org/data_0875' - Label 'Protein topology'\n", + "Entity 'http://edamontology.org/data_0876' - Label 'Protein features report (secondary structure)'\n", + "Entity 'http://edamontology.org/data_0876' - Label 'Protein features report (secondary structure)'\n", + "Entity 'http://edamontology.org/data_0877' - Label 'Protein features report (super-secondary)'\n", + "Entity 'http://edamontology.org/data_0877' - Label 'Protein features report (super-secondary)'\n", + "Entity 'http://edamontology.org/data_0878' - Label 'Protein secondary structure alignment'\n", + "Entity 'http://edamontology.org/data_0879' - Label 'Secondary structure alignment metadata (protein)'\n", + "Entity 'http://edamontology.org/data_0879' - Label 'Secondary structure alignment metadata (protein)'\n", + "Entity 'http://edamontology.org/data_0880' - Label 'RNA secondary structure'\n", + "Entity 'http://edamontology.org/data_0880' - Label 'RNA secondary structure'\n", + "Entity 'http://edamontology.org/data_0881' - Label 'RNA secondary structure alignment'\n", + "Entity 'http://edamontology.org/data_0882' - Label 'Secondary structure alignment metadata (RNA)'\n", + "Entity 'http://edamontology.org/data_0882' - Label 'Secondary structure alignment metadata (RNA)'\n", + "Entity 'http://edamontology.org/data_0883' - Label 'Structure'\n", + "Entity 'http://edamontology.org/data_0883' - Label 'Structure'\n", + "Entity 'http://edamontology.org/data_0884' - Label 'Tertiary structure record'\n", + "Entity 'http://edamontology.org/data_0884' - Label 'Tertiary structure record'\n", + "Entity 'http://edamontology.org/data_0885' - Label 'Structure database search results'\n", + "Entity 'http://edamontology.org/data_0885' - Label 'Structure database search results'\n", + "Entity 'http://edamontology.org/data_0886' - Label 'Structure alignment'\n", + "Entity 'http://edamontology.org/data_0886' - Label 'Structure alignment'\n", + "Entity 'http://edamontology.org/data_0887' - Label 'Structure alignment report'\n", + "Entity 'http://edamontology.org/data_0888' - Label 'Structure similarity score'\n", + "Entity 'http://edamontology.org/data_0889' - Label 'Structural profile'\n", + "Entity 'http://edamontology.org/data_0889' - Label 'Structural profile'\n", + "Entity 'http://edamontology.org/data_0890' - Label 'Structural (3D) profile alignment'\n", + "Entity 'http://edamontology.org/data_0891' - Label 'Sequence-3D profile alignment'\n", + "Entity 'http://edamontology.org/data_0891' - Label 'Sequence-3D profile alignment'\n", + "Entity 'http://edamontology.org/data_0892' - Label 'Protein sequence-structure scoring matrix'\n", + "Entity 'http://edamontology.org/data_0893' - Label 'Sequence-structure alignment'\n", + "Entity 'http://edamontology.org/data_0894' - Label 'Amino acid annotation'\n", + "Entity 'http://edamontology.org/data_0894' - Label 'Amino acid annotation'\n", + "Entity 'http://edamontology.org/data_0895' - Label 'Peptide annotation'\n", + "Entity 'http://edamontology.org/data_0895' - Label 'Peptide annotation'\n", + "Entity 'http://edamontology.org/data_0896' - Label 'Protein report'\n", + "Entity 'http://edamontology.org/data_0897' - Label 'Protein property'\n", + "Entity 'http://edamontology.org/data_0899' - Label 'Protein structural motifs and surfaces'\n", + "Entity 'http://edamontology.org/data_0899' - Label 'Protein structural motifs and surfaces'\n", + "Entity 'http://edamontology.org/data_0900' - Label 'Protein domain classification'\n", + "Entity 'http://edamontology.org/data_0900' - Label 'Protein domain classification'\n", + "Entity 'http://edamontology.org/data_0901' - Label 'Protein features report (domains)'\n", + "Entity 'http://edamontology.org/data_0901' - Label 'Protein features report (domains)'\n", + "Entity 'http://edamontology.org/data_0902' - Label 'Protein architecture report'\n", + "Entity 'http://edamontology.org/data_0902' - Label 'Protein architecture report'\n", + "Entity 'http://edamontology.org/data_0903' - Label 'Protein folding report'\n", + "Entity 'http://edamontology.org/data_0903' - Label 'Protein folding report'\n", + "Entity 'http://edamontology.org/data_0904' - Label 'Protein features (mutation)'\n", + "Entity 'http://edamontology.org/data_0904' - Label 'Protein features (mutation)'\n", + "Entity 'http://edamontology.org/data_0905' - Label 'Protein interaction raw data'\n", + "Entity 'http://edamontology.org/data_0906' - Label 'Protein interaction data'\n", + "Entity 'http://edamontology.org/data_0906' - Label 'Protein interaction data'\n", + "Entity 'http://edamontology.org/data_0907' - Label 'Protein family report'\n", + "Entity 'http://edamontology.org/data_0907' - Label 'Protein family report'\n", + "Entity 'http://edamontology.org/data_0909' - Label 'Vmax'\n", + "Entity 'http://edamontology.org/data_0910' - Label 'Km'\n", + "Entity 'http://edamontology.org/data_0911' - Label 'Nucleotide base annotation'\n", + "Entity 'http://edamontology.org/data_0911' - Label 'Nucleotide base annotation'\n", + "Entity 'http://edamontology.org/data_0912' - Label 'Nucleic acid property'\n", + "Entity 'http://edamontology.org/data_0914' - Label 'Codon usage data'\n", + "Entity 'http://edamontology.org/data_0914' - Label 'Codon usage data'\n", + "Entity 'http://edamontology.org/data_0916' - Label 'Gene report'\n", + "Entity 'http://edamontology.org/data_0917' - Label 'Gene classification'\n", + "Entity 'http://edamontology.org/data_0917' - Label 'Gene classification'\n", + "Entity 'http://edamontology.org/data_0918' - Label 'DNA variation'\n", + "Entity 'http://edamontology.org/data_0918' - Label 'DNA variation'\n", + "Entity 'http://edamontology.org/data_0919' - Label 'Chromosome report'\n", + "Entity 'http://edamontology.org/data_0920' - Label 'Genotype/phenotype report'\n", + "Entity 'http://edamontology.org/data_0923' - Label 'PCR experiment report'\n", + "Entity 'http://edamontology.org/data_0923' - Label 'PCR experiment report'\n", + "Entity 'http://edamontology.org/data_0924' - Label 'Sequence trace'\n", + "Entity 'http://edamontology.org/data_0924' - Label 'Sequence trace'\n", + "Entity 'http://edamontology.org/data_0925' - Label 'Sequence assembly'\n", + "Entity 'http://edamontology.org/data_0926' - Label 'RH scores'\n", + "Entity 'http://edamontology.org/data_0927' - Label 'Genetic linkage report'\n", + "Entity 'http://edamontology.org/data_0928' - Label 'Gene expression profile'\n", + "Entity 'http://edamontology.org/data_0931' - Label 'Microarray experiment report'\n", + "Entity 'http://edamontology.org/data_0931' - Label 'Microarray experiment report'\n", + "Entity 'http://edamontology.org/data_0932' - Label 'Oligonucleotide probe data'\n", + "Entity 'http://edamontology.org/data_0932' - Label 'Oligonucleotide probe data'\n", + "Entity 'http://edamontology.org/data_0933' - Label 'SAGE experimental data'\n", + "Entity 'http://edamontology.org/data_0933' - Label 'SAGE experimental data'\n", + "Entity 'http://edamontology.org/data_0934' - Label 'MPSS experimental data'\n", + "Entity 'http://edamontology.org/data_0934' - Label 'MPSS experimental data'\n", + "Entity 'http://edamontology.org/data_0935' - Label 'SBS experimental data'\n", + "Entity 'http://edamontology.org/data_0935' - Label 'SBS experimental data'\n", + "Entity 'http://edamontology.org/data_0936' - Label 'Sequence tag profile (with gene assignment)'\n", + "Entity 'http://edamontology.org/data_0936' - Label 'Sequence tag profile (with gene assignment)'\n", + "Entity 'http://edamontology.org/data_0937' - Label 'Electron density map'\n", + "Entity 'http://edamontology.org/data_0938' - Label 'Raw NMR data'\n", + "Entity 'http://edamontology.org/data_0939' - Label 'CD spectra'\n", + "Entity 'http://edamontology.org/data_0940' - Label 'Volume map'\n", + "Entity 'http://edamontology.org/data_0940' - Label 'Volume map'\n", + "Entity 'http://edamontology.org/data_0941' - Label 'Electron microscopy model'\n", + "Entity 'http://edamontology.org/data_0941' - Label 'Electron microscopy model'\n", + "Entity 'http://edamontology.org/data_0942' - Label '2D PAGE image'\n", + "Entity 'http://edamontology.org/data_0942' - Label '2D PAGE image'\n", + "Entity 'http://edamontology.org/data_0943' - Label 'Mass spectrum'\n", + "Entity 'http://edamontology.org/data_0943' - Label 'Mass spectrum'\n", + "Entity 'http://edamontology.org/data_0944' - Label 'Peptide mass fingerprint'\n", + "Entity 'http://edamontology.org/data_0944' - Label 'Peptide mass fingerprint'\n", + "Entity 'http://edamontology.org/data_0944' - Label 'Peptide mass fingerprint'\n", + "Entity 'http://edamontology.org/data_0945' - Label 'Peptide identification'\n", + "Entity 'http://edamontology.org/data_0945' - Label 'Peptide identification'\n", + "Entity 'http://edamontology.org/data_0945' - Label 'Peptide identification'\n", + "Entity 'http://edamontology.org/data_0946' - Label 'Pathway or network annotation'\n", + "Entity 'http://edamontology.org/data_0946' - Label 'Pathway or network annotation'\n", + "Entity 'http://edamontology.org/data_0947' - Label 'Biological pathway map'\n", + "Entity 'http://edamontology.org/data_0947' - Label 'Biological pathway map'\n", + "Entity 'http://edamontology.org/data_0948' - Label 'Data resource definition'\n", + "Entity 'http://edamontology.org/data_0948' - Label 'Data resource definition'\n", + "Entity 'http://edamontology.org/data_0949' - Label 'Workflow metadata'\n", + "Entity 'http://edamontology.org/data_0950' - Label 'Mathematical model'\n", + "Entity 'http://edamontology.org/data_0950' - Label 'Mathematical model'\n", + "Entity 'http://edamontology.org/data_0951' - Label 'Statistical estimate score'\n", + "Entity 'http://edamontology.org/data_0952' - Label 'EMBOSS database resource definition'\n", + "Entity 'http://edamontology.org/data_0952' - Label 'EMBOSS database resource definition'\n", + "Entity 'http://edamontology.org/data_0953' - Label 'Version information'\n", + "Entity 'http://edamontology.org/data_0953' - Label 'Version information'\n", + "Entity 'http://edamontology.org/data_0954' - Label 'Database cross-mapping'\n", + "Entity 'http://edamontology.org/data_0955' - Label 'Data index'\n", + "Entity 'http://edamontology.org/data_0955' - Label 'Data index'\n", + "Entity 'http://edamontology.org/data_0956' - Label 'Data index report'\n", + "Entity 'http://edamontology.org/data_0956' - Label 'Data index report'\n", + "Entity 'http://edamontology.org/data_0957' - Label 'Database metadata'\n", + "Entity 'http://edamontology.org/data_0958' - Label 'Tool metadata'\n", + "Entity 'http://edamontology.org/data_0959' - Label 'Job metadata'\n", + "Entity 'http://edamontology.org/data_0959' - Label 'Job metadata'\n", + "Entity 'http://edamontology.org/data_0960' - Label 'User metadata'\n", + "Entity 'http://edamontology.org/data_0962' - Label 'Small molecule report'\n", + "Entity 'http://edamontology.org/data_0962' - Label 'Small molecule report'\n", + "Entity 'http://edamontology.org/data_0963' - Label 'Cell line report'\n", + "Entity 'http://edamontology.org/data_0964' - Label 'Scent annotation'\n", + "Entity 'http://edamontology.org/data_0964' - Label 'Scent annotation'\n", + "Entity 'http://edamontology.org/data_0966' - Label 'Ontology term'\n", + "Entity 'http://edamontology.org/data_0967' - Label 'Ontology concept data'\n", + "Entity 'http://edamontology.org/data_0968' - Label 'Keyword'\n", + "Entity 'http://edamontology.org/data_0970' - Label 'Citation'\n", + "Entity 'http://edamontology.org/data_0971' - Label 'Article'\n", + "Entity 'http://edamontology.org/data_0971' - Label 'Article'\n", + "Entity 'http://edamontology.org/data_0972' - Label 'Text mining report'\n", + "Entity 'http://edamontology.org/data_0972' - Label 'Text mining report'\n", + "Entity 'http://edamontology.org/data_0974' - Label 'Entity identifier'\n", + "Entity 'http://edamontology.org/data_0974' - Label 'Entity identifier'\n", + "Entity 'http://edamontology.org/data_0975' - Label 'Data resource identifier'\n", + "Entity 'http://edamontology.org/data_0975' - Label 'Data resource identifier'\n", + "Entity 'http://edamontology.org/data_0976' - Label 'Identifier (by type of entity)'\n", + "Entity 'http://edamontology.org/data_0977' - Label 'Tool identifier'\n", + "Entity 'http://edamontology.org/data_0978' - Label 'Discrete entity identifier'\n", + "Entity 'http://edamontology.org/data_0978' - Label 'Discrete entity identifier'\n", + "Entity 'http://edamontology.org/data_0979' - Label 'Entity feature identifier'\n", + "Entity 'http://edamontology.org/data_0979' - Label 'Entity feature identifier'\n", + "Entity 'http://edamontology.org/data_0980' - Label 'Entity collection identifier'\n", + "Entity 'http://edamontology.org/data_0980' - Label 'Entity collection identifier'\n", + "Entity 'http://edamontology.org/data_0981' - Label 'Phenomenon identifier'\n", + "Entity 'http://edamontology.org/data_0981' - Label 'Phenomenon identifier'\n", + "Entity 'http://edamontology.org/data_0982' - Label 'Molecule identifier'\n", + "Entity 'http://edamontology.org/data_0983' - Label 'Atom ID'\n", + "Entity 'http://edamontology.org/data_0984' - Label 'Molecule name'\n", + "Entity 'http://edamontology.org/data_0984' - Label 'Molecule name'\n", + "Entity 'http://edamontology.org/data_0985' - Label 'Molecule type'\n", + "Entity 'http://edamontology.org/data_0985' - Label 'Molecule type'\n", + "Entity 'http://edamontology.org/data_0986' - Label 'Chemical identifier'\n", + "Entity 'http://edamontology.org/data_0986' - Label 'Chemical identifier'\n", + "Entity 'http://edamontology.org/data_0987' - Label 'Chromosome name'\n", + "Entity 'http://edamontology.org/data_0987' - Label 'Chromosome name'\n", + "Entity 'http://edamontology.org/data_0987' - Label 'Chromosome name'\n", + "Entity 'http://edamontology.org/data_0988' - Label 'Peptide identifier'\n", + "Entity 'http://edamontology.org/data_0989' - Label 'Protein identifier'\n", + "Entity 'http://edamontology.org/data_0989' - Label 'Protein identifier'\n", + "Entity 'http://edamontology.org/data_0990' - Label 'Compound name'\n", + "Entity 'http://edamontology.org/data_0990' - Label 'Compound name'\n", + "Entity 'http://edamontology.org/data_0991' - Label 'Chemical registry number'\n", + "Entity 'http://edamontology.org/data_0992' - Label 'Ligand identifier'\n", + "Entity 'http://edamontology.org/data_0992' - Label 'Ligand identifier'\n", + "Entity 'http://edamontology.org/data_0993' - Label 'Drug identifier'\n", + "Entity 'http://edamontology.org/data_0993' - Label 'Drug identifier'\n", + "Entity 'http://edamontology.org/data_0994' - Label 'Amino acid identifier'\n", + "Entity 'http://edamontology.org/data_0994' - Label 'Amino acid identifier'\n", + "Entity 'http://edamontology.org/data_0995' - Label 'Nucleotide identifier'\n", + "Entity 'http://edamontology.org/data_0996' - Label 'Monosaccharide identifier'\n", + "Entity 'http://edamontology.org/data_0997' - Label 'Chemical name (ChEBI)'\n", + "Entity 'http://edamontology.org/data_0998' - Label 'Chemical name (IUPAC)'\n", + "Entity 'http://edamontology.org/data_0999' - Label 'Chemical name (INN)'\n", + "Entity 'http://edamontology.org/data_1000' - Label 'Chemical name (brand)'\n", + "Entity 'http://edamontology.org/data_1001' - Label 'Chemical name (synonymous)'\n", + "Entity 'http://edamontology.org/data_1002' - Label 'CAS number'\n", + "Entity 'http://edamontology.org/data_1002' - Label 'CAS number'\n", + "Entity 'http://edamontology.org/data_1002' - Label 'CAS number'\n", + "Entity 'http://edamontology.org/data_1003' - Label 'Chemical registry number (Beilstein)'\n", + "Entity 'http://edamontology.org/data_1003' - Label 'Chemical registry number (Beilstein)'\n", + "Entity 'http://edamontology.org/data_1004' - Label 'Chemical registry number (Gmelin)'\n", + "Entity 'http://edamontology.org/data_1004' - Label 'Chemical registry number (Gmelin)'\n", + "Entity 'http://edamontology.org/data_1005' - Label 'HET group name'\n", + "Entity 'http://edamontology.org/data_1006' - 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Label 'Gene synonym'\n", + "Entity 'http://edamontology.org/data_1806' - Label 'Gene synonym'\n", + "Entity 'http://edamontology.org/data_1807' - Label 'ORF name'\n", + "Entity 'http://edamontology.org/data_1807' - Label 'ORF name'\n", + "Entity 'http://edamontology.org/data_1852' - Label 'Sequence assembly component'\n", + "Entity 'http://edamontology.org/data_1852' - Label 'Sequence assembly component'\n", + "Entity 'http://edamontology.org/data_1853' - Label 'Chromosome annotation (aberration)'\n", + "Entity 'http://edamontology.org/data_1853' - Label 'Chromosome annotation (aberration)'\n", + "Entity 'http://edamontology.org/data_1855' - Label 'Clone ID'\n", + "Entity 'http://edamontology.org/data_1856' - Label 'PDB insertion code'\n", + "Entity 'http://edamontology.org/data_1857' - Label 'Atomic occupancy'\n", + "Entity 'http://edamontology.org/data_1858' - Label 'Isotropic B factor'\n", + "Entity 'http://edamontology.org/data_1859' - Label 'Deletion map'\n", + "Entity 'http://edamontology.org/data_1860' - Label 'QTL map'\n", + "Entity 'http://edamontology.org/data_1863' - Label 'Haplotype map'\n", + "Entity 'http://edamontology.org/data_1864' - Label 'Map set data'\n", + "Entity 'http://edamontology.org/data_1864' - Label 'Map set data'\n", + "Entity 'http://edamontology.org/data_1865' - Label 'Map feature'\n", + "Entity 'http://edamontology.org/data_1865' - Label 'Map feature'\n", + "Entity 'http://edamontology.org/data_1865' - Label 'Map feature'\n", + "Entity 'http://edamontology.org/data_1865' - Label 'Map feature'\n", + "Entity 'http://edamontology.org/data_1866' - Label 'Map type'\n", + "Entity 'http://edamontology.org/data_1866' - Label 'Map type'\n", + "Entity 'http://edamontology.org/data_1867' - Label 'Protein fold name'\n", + "Entity 'http://edamontology.org/data_1868' - Label 'Taxon'\n", + "Entity 'http://edamontology.org/data_1869' - Label 'Organism identifier'\n", + "Entity 'http://edamontology.org/data_1869' - Label 'Organism identifier'\n", + "Entity 'http://edamontology.org/data_1870' - Label 'Genus name'\n", + "Entity 'http://edamontology.org/data_1872' - Label 'Taxonomic classification'\n", + "Entity 'http://edamontology.org/data_1873' - Label 'iHOP organism ID'\n", + "Entity 'http://edamontology.org/data_1873' - Label 'iHOP organism ID'\n", + "Entity 'http://edamontology.org/data_1874' - Label 'Genbank common name'\n", + "Entity 'http://edamontology.org/data_1875' - Label 'NCBI taxon'\n", + "Entity 'http://edamontology.org/data_1877' - Label 'Synonym'\n", + "Entity 'http://edamontology.org/data_1877' - Label 'Synonym'\n", + "Entity 'http://edamontology.org/data_1878' - Label 'Misspelling'\n", + "Entity 'http://edamontology.org/data_1878' - Label 'Misspelling'\n", + "Entity 'http://edamontology.org/data_1879' - Label 'Acronym'\n", + "Entity 'http://edamontology.org/data_1879' - Label 'Acronym'\n", + "Entity 'http://edamontology.org/data_1880' - Label 'Misnomer'\n", + "Entity 'http://edamontology.org/data_1880' - Label 'Misnomer'\n", + "Entity 'http://edamontology.org/data_1881' - Label 'Author ID'\n", + "Entity 'http://edamontology.org/data_1882' - Label 'DragonDB author identifier'\n", + "Entity 'http://edamontology.org/data_1883' - Label 'Annotated URI'\n", + "Entity 'http://edamontology.org/data_1884' - Label 'UniProt keywords'\n", + "Entity 'http://edamontology.org/data_1884' - Label 'UniProt keywords'\n", + "Entity 'http://edamontology.org/data_1885' - Label 'Gene ID (GeneFarm)'\n", + "Entity 'http://edamontology.org/data_1885' - Label 'Gene ID (GeneFarm)'\n", + "Entity 'http://edamontology.org/data_1886' - Label 'Blattner number'\n", + "Entity 'http://edamontology.org/data_1886' - Label 'Blattner number'\n", + "Entity 'http://edamontology.org/data_1887' - Label 'Gene ID (MIPS Maize)'\n", + "Entity 'http://edamontology.org/data_1887' - Label 'Gene ID (MIPS Maize)'\n", + "Entity 'http://edamontology.org/data_1888' - Label 'Gene ID (MIPS Medicago)'\n", + "Entity 'http://edamontology.org/data_1888' - Label 'Gene ID (MIPS Medicago)'\n", + "Entity 'http://edamontology.org/data_1889' - Label 'Gene name (DragonDB)'\n", + "Entity 'http://edamontology.org/data_1889' - Label 'Gene name (DragonDB)'\n", + "Entity 'http://edamontology.org/data_1890' - Label 'Gene name (Arabidopsis)'\n", + "Entity 'http://edamontology.org/data_1890' - Label 'Gene name (Arabidopsis)'\n", + "Entity 'http://edamontology.org/data_1891' - Label 'iHOP symbol'\n", + "Entity 'http://edamontology.org/data_1891' - Label 'iHOP symbol'\n", + "Entity 'http://edamontology.org/data_1891' - Label 'iHOP symbol'\n", + "Entity 'http://edamontology.org/data_1891' - Label 'iHOP symbol'\n", + "Entity 'http://edamontology.org/data_1892' - Label 'Gene name (GeneFarm)'\n", + "Entity 'http://edamontology.org/data_1892' - Label 'Gene name (GeneFarm)'\n", + "Entity 'http://edamontology.org/data_1893' - Label 'Locus ID'\n", + "Entity 'http://edamontology.org/data_1893' - Label 'Locus ID'\n", + "Entity 'http://edamontology.org/data_1895' - Label 'Locus ID (AGI)'\n", + "Entity 'http://edamontology.org/data_1895' - Label 'Locus ID (AGI)'\n", + "Entity 'http://edamontology.org/data_1896' - Label 'Locus ID (ASPGD)'\n", + "Entity 'http://edamontology.org/data_1896' - Label 'Locus ID (ASPGD)'\n", + "Entity 'http://edamontology.org/data_1897' - Label 'Locus ID (MGG)'\n", + "Entity 'http://edamontology.org/data_1897' - Label 'Locus ID (MGG)'\n", + "Entity 'http://edamontology.org/data_1898' - Label 'Locus ID (CGD)'\n", + "Entity 'http://edamontology.org/data_1898' - Label 'Locus ID (CGD)'\n", + "Entity 'http://edamontology.org/data_1899' - Label 'Locus ID (CMR)'\n", + "Entity 'http://edamontology.org/data_1899' - Label 'Locus ID (CMR)'\n", + "Entity 'http://edamontology.org/data_1900' - Label 'NCBI locus tag'\n", + "Entity 'http://edamontology.org/data_1900' - Label 'NCBI locus tag'\n", + "Entity 'http://edamontology.org/data_1901' - Label 'Locus ID (SGD)'\n", + "Entity 'http://edamontology.org/data_1901' - Label 'Locus ID (SGD)'\n", + "Entity 'http://edamontology.org/data_1901' - Label 'Locus ID (SGD)'\n", + "Entity 'http://edamontology.org/data_1902' - Label 'Locus ID (MMP)'\n", + "Entity 'http://edamontology.org/data_1902' - Label 'Locus ID (MMP)'\n", + "Entity 'http://edamontology.org/data_1903' - Label 'Locus ID (DictyBase)'\n", + "Entity 'http://edamontology.org/data_1903' - Label 'Locus ID (DictyBase)'\n", + "Entity 'http://edamontology.org/data_1904' - Label 'Locus ID (EntrezGene)'\n", + "Entity 'http://edamontology.org/data_1904' - Label 'Locus ID (EntrezGene)'\n", + "Entity 'http://edamontology.org/data_1905' - Label 'Locus ID (MaizeGDB)'\n", + "Entity 'http://edamontology.org/data_1905' - Label 'Locus ID (MaizeGDB)'\n", + "Entity 'http://edamontology.org/data_1906' - Label 'Quantitative trait locus'\n", + "Entity 'http://edamontology.org/data_1906' - Label 'Quantitative trait locus'\n", + "Entity 'http://edamontology.org/data_1907' - Label 'Gene ID (KOME)'\n", + "Entity 'http://edamontology.org/data_1907' - Label 'Gene ID (KOME)'\n", + "Entity 'http://edamontology.org/data_1908' - Label 'Locus ID (Tropgene)'\n", + "Entity 'http://edamontology.org/data_1908' - Label 'Locus ID (Tropgene)'\n", + "Entity 'http://edamontology.org/data_1916' - Label 'Alignment'\n", + "Entity 'http://edamontology.org/data_1917' - Label 'Atomic property'\n", + "Entity 'http://edamontology.org/data_2007' - Label 'UniProt keyword'\n", + "Entity 'http://edamontology.org/data_2009' - Label 'Ordered locus name'\n", + "Entity 'http://edamontology.org/data_2009' - Label 'Ordered locus name'\n", + "Entity 'http://edamontology.org/data_2012' - Label 'Sequence coordinates'\n", + "Entity 'http://edamontology.org/data_2012' - Label 'Sequence coordinates'\n", + "Entity 'http://edamontology.org/data_2012' - Label 'Sequence coordinates'\n", + "Entity 'http://edamontology.org/data_2016' - Label 'Amino acid property'\n", + "Entity 'http://edamontology.org/data_2018' - Label 'Annotation'\n", + "Entity 'http://edamontology.org/data_2018' - Label 'Annotation'\n", + "Entity 'http://edamontology.org/data_2019' - Label 'Map data'\n", + "Entity 'http://edamontology.org/data_2019' - Label 'Map data'\n", + "Entity 'http://edamontology.org/data_2022' - Label 'Vienna RNA structural data'\n", + "Entity 'http://edamontology.org/data_2022' - Label 'Vienna RNA structural data'\n", + "Entity 'http://edamontology.org/data_2023' - Label 'Sequence mask parameter'\n", + "Entity 'http://edamontology.org/data_2023' - Label 'Sequence mask parameter'\n", + "Entity 'http://edamontology.org/data_2024' - Label 'Enzyme kinetics data'\n", + "Entity 'http://edamontology.org/data_2024' - Label 'Enzyme kinetics data'\n", + "Entity 'http://edamontology.org/data_2025' - Label 'Michaelis Menten plot'\n", + "Entity 'http://edamontology.org/data_2026' - Label 'Hanes Woolf plot'\n", + "Entity 'http://edamontology.org/data_2028' - Label 'Experimental data'\n", + "Entity 'http://edamontology.org/data_2028' - Label 'Experimental data'\n", + "Entity 'http://edamontology.org/data_2028' - Label 'Experimental data'\n", + "Entity 'http://edamontology.org/data_2041' - Label 'Genome version information'\n", + "Entity 'http://edamontology.org/data_2041' - Label 'Genome version information'\n", + "Entity 'http://edamontology.org/data_2042' - Label 'Evidence'\n", + "Entity 'http://edamontology.org/data_2043' - Label 'Sequence record lite'\n", + "Entity 'http://edamontology.org/data_2043' - Label 'Sequence record lite'\n", + "Entity 'http://edamontology.org/data_2044' - Label 'Sequence'\n", + "Entity 'http://edamontology.org/data_2044' - Label 'Sequence'\n", + "Entity 'http://edamontology.org/data_2046' - Label 'Nucleic acid sequence record (lite)'\n", + "Entity 'http://edamontology.org/data_2046' - Label 'Nucleic acid sequence record (lite)'\n", + "Entity 'http://edamontology.org/data_2047' - Label 'Protein sequence record (lite)'\n", + "Entity 'http://edamontology.org/data_2047' - Label 'Protein sequence record (lite)'\n", + "Entity 'http://edamontology.org/data_2048' - Label 'Report'\n", + "Entity 'http://edamontology.org/data_2050' - Label 'Molecular property (general)'\n", + "Entity 'http://edamontology.org/data_2053' - Label 'Structural data'\n", + "Entity 'http://edamontology.org/data_2053' - Label 'Structural data'\n", + "Entity 'http://edamontology.org/data_2053' - Label 'Structural data'\n", + "Entity 'http://edamontology.org/data_2070' - Label 'Sequence motif (nucleic acid)'\n", + "Entity 'http://edamontology.org/data_2071' - Label 'Sequence motif (protein)'\n", + "Entity 'http://edamontology.org/data_2079' - Label 'Search parameter'\n", + "Entity 'http://edamontology.org/data_2079' - Label 'Search parameter'\n", + "Entity 'http://edamontology.org/data_2080' - Label 'Database search results'\n", + "Entity 'http://edamontology.org/data_2081' - Label 'Secondary structure'\n", + "Entity 'http://edamontology.org/data_2081' - Label 'Secondary structure'\n", + "Entity 'http://edamontology.org/data_2082' - Label 'Matrix'\n", + "Entity 'http://edamontology.org/data_2083' - Label 'Alignment data'\n", + "Entity 'http://edamontology.org/data_2083' - Label 'Alignment data'\n", + "Entity 'http://edamontology.org/data_2084' - Label 'Nucleic acid report'\n", + "Entity 'http://edamontology.org/data_2085' - Label 'Structure report'\n", + "Entity 'http://edamontology.org/data_2086' - Label 'Nucleic acid structure data'\n", + "Entity 'http://edamontology.org/data_2086' - Label 'Nucleic acid structure data'\n", + "Entity 'http://edamontology.org/data_2086' - Label 'Nucleic acid structure data'\n", + "Entity 'http://edamontology.org/data_2087' - Label 'Molecular property'\n", + "Entity 'http://edamontology.org/data_2088' - Label 'DNA base structural data'\n", + "Entity 'http://edamontology.org/data_2090' - Label 'Database entry version information'\n", + "Entity 'http://edamontology.org/data_2090' - Label 'Database entry version information'\n", + "Entity 'http://edamontology.org/data_2091' - Label 'Accession'\n", + "Entity 'http://edamontology.org/data_2092' - Label 'SNP'\n", + "Entity 'http://edamontology.org/data_2092' - Label 'SNP'\n", + "Entity 'http://edamontology.org/data_2093' - Label 'Data reference'\n", + "Entity 'http://edamontology.org/data_2098' - Label 'Job identifier'\n", + "Entity 'http://edamontology.org/data_2099' - Label 'Name'\n", + "Entity 'http://edamontology.org/data_2100' - Label 'Type'\n", + "Entity 'http://edamontology.org/data_2100' - Label 'Type'\n", + "Entity 'http://edamontology.org/data_2101' - Label 'Account authentication'\n", + "Entity 'http://edamontology.org/data_2102' - Label 'KEGG organism code'\n", + "Entity 'http://edamontology.org/data_2102' - Label 'KEGG organism code'\n", + "Entity 'http://edamontology.org/data_2103' - Label 'Gene name (KEGG GENES)'\n", + "Entity 'http://edamontology.org/data_2103' - Label 'Gene name (KEGG GENES)'\n", + "Entity 'http://edamontology.org/data_2104' - Label 'BioCyc ID'\n", + "Entity 'http://edamontology.org/data_2104' - Label 'BioCyc ID'\n", + "Entity 'http://edamontology.org/data_2105' - Label 'Compound ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2105' - Label 'Compound ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2105' - Label 'Compound ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2106' - Label 'Reaction ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2106' - Label 'Reaction ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2106' - Label 'Reaction ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2107' - Label 'Enzyme ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2107' - Label 'Enzyme ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2107' - Label 'Enzyme ID (BioCyc)'\n", + "Entity 'http://edamontology.org/data_2108' - Label 'Reaction ID'\n", + "Entity 'http://edamontology.org/data_2108' - Label 'Reaction ID'\n", + "Entity 'http://edamontology.org/data_2109' - Label 'Identifier (hybrid)'\n", + "Entity 'http://edamontology.org/data_2110' - Label 'Molecular property identifier'\n", + "Entity 'http://edamontology.org/data_2110' - Label 'Molecular property identifier'\n", + "Entity 'http://edamontology.org/data_2111' - Label 'Codon usage table ID'\n", + "Entity 'http://edamontology.org/data_2111' - Label 'Codon usage table ID'\n", + "Entity 'http://edamontology.org/data_2111' - Label 'Codon usage table ID'\n", + "Entity 'http://edamontology.org/data_2112' - Label 'FlyBase primary identifier'\n", + "Entity 'http://edamontology.org/data_2113' - Label 'WormBase identifier'\n", + "Entity 'http://edamontology.org/data_2114' - Label 'WormBase wormpep ID'\n", + "Entity 'http://edamontology.org/data_2114' - Label 'WormBase wormpep ID'\n", + "Entity 'http://edamontology.org/data_2114' - Label 'WormBase wormpep ID'\n", + "Entity 'http://edamontology.org/data_2116' - Label 'Nucleic acid features (codon)'\n", + "Entity 'http://edamontology.org/data_2116' - Label 'Nucleic acid features (codon)'\n", + "Entity 'http://edamontology.org/data_2117' - Label 'Map identifier'\n", + "Entity 'http://edamontology.org/data_2117' - Label 'Map identifier'\n", + "Entity 'http://edamontology.org/data_2118' - Label 'Person identifier'\n", + "Entity 'http://edamontology.org/data_2119' - Label 'Nucleic acid identifier'\n", + "Entity 'http://edamontology.org/data_2119' - Label 'Nucleic acid identifier'\n", + "Entity 'http://edamontology.org/data_2126' - Label 'Translation frame specification'\n", + "Entity 'http://edamontology.org/data_2126' - Label 'Translation frame specification'\n", + "Entity 'http://edamontology.org/data_2127' - Label 'Genetic code identifier'\n", + "Entity 'http://edamontology.org/data_2127' - Label 'Genetic code identifier'\n", + "Entity 'http://edamontology.org/data_2128' - Label 'Genetic code name'\n", + "Entity 'http://edamontology.org/data_2128' - Label 'Genetic code name'\n", + "Entity 'http://edamontology.org/data_2129' - Label 'File format name'\n", + "Entity 'http://edamontology.org/data_2129' - Label 'File format name'\n", + "Entity 'http://edamontology.org/data_2130' - Label 'Sequence profile type'\n", + "Entity 'http://edamontology.org/data_2130' - Label 'Sequence profile type'\n", + "Entity 'http://edamontology.org/data_2131' - Label 'Operating system name'\n", + "Entity 'http://edamontology.org/data_2132' - Label 'Mutation type'\n", + "Entity 'http://edamontology.org/data_2132' - Label 'Mutation type'\n", + "Entity 'http://edamontology.org/data_2133' - Label 'Logical operator'\n", + "Entity 'http://edamontology.org/data_2134' - Label 'Results sort order'\n", + "Entity 'http://edamontology.org/data_2134' - Label 'Results sort order'\n", + "Entity 'http://edamontology.org/data_2135' - Label 'Toggle'\n", + "Entity 'http://edamontology.org/data_2135' - Label 'Toggle'\n", + "Entity 'http://edamontology.org/data_2136' - Label 'Sequence width'\n", + "Entity 'http://edamontology.org/data_2136' - Label 'Sequence width'\n", + "Entity 'http://edamontology.org/data_2137' - Label 'Gap penalty'\n", + "Entity 'http://edamontology.org/data_2139' - Label 'Nucleic acid melting temperature'\n", + "Entity 'http://edamontology.org/data_2140' - Label 'Concentration'\n", + "Entity 'http://edamontology.org/data_2141' - Label 'Window step size'\n", + "Entity 'http://edamontology.org/data_2141' - Label 'Window step size'\n", + "Entity 'http://edamontology.org/data_2142' - Label 'EMBOSS graph'\n", + "Entity 'http://edamontology.org/data_2142' - Label 'EMBOSS graph'\n", + "Entity 'http://edamontology.org/data_2143' - Label 'EMBOSS report'\n", + "Entity 'http://edamontology.org/data_2143' - Label 'EMBOSS report'\n", + "Entity 'http://edamontology.org/data_2145' - 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Label 'Amino acid name (three letter)'\n", + "Entity 'http://edamontology.org/data_2565' - Label 'Amino acid name (full name)'\n", + "Entity 'http://edamontology.org/data_2576' - Label 'Toxin identifier'\n", + "Entity 'http://edamontology.org/data_2576' - Label 'Toxin identifier'\n", + "Entity 'http://edamontology.org/data_2578' - Label 'ArachnoServer ID'\n", + "Entity 'http://edamontology.org/data_2578' - Label 'ArachnoServer ID'\n", + "Entity 'http://edamontology.org/data_2579' - Label 'Expressed gene list'\n", + "Entity 'http://edamontology.org/data_2579' - Label 'Expressed gene list'\n", + "Entity 'http://edamontology.org/data_2580' - Label 'BindingDB Monomer ID'\n", + "Entity 'http://edamontology.org/data_2580' - Label 'BindingDB Monomer ID'\n", + "Entity 'http://edamontology.org/data_2581' - Label 'GO concept name'\n", + "Entity 'http://edamontology.org/data_2581' - Label 'GO concept name'\n", + "Entity 'http://edamontology.org/data_2582' - Label 'GO concept ID (biological process)'\n", + "Entity 'http://edamontology.org/data_2583' - Label 'GO concept ID (molecular function)'\n", + "Entity 'http://edamontology.org/data_2584' - Label 'GO concept name (cellular component)'\n", + "Entity 'http://edamontology.org/data_2584' - Label 'GO concept name (cellular component)'\n", + "Entity 'http://edamontology.org/data_2586' - Label 'Northern blot image'\n", + "Entity 'http://edamontology.org/data_2587' - Label 'Blot ID'\n", + "Entity 'http://edamontology.org/data_2588' - Label 'BlotBase blot ID'\n", + "Entity 'http://edamontology.org/data_2588' - Label 'BlotBase blot ID'\n", + "Entity 'http://edamontology.org/data_2589' - Label 'Hierarchy'\n", + "Entity 'http://edamontology.org/data_2590' - Label 'Hierarchy identifier'\n", + "Entity 'http://edamontology.org/data_2590' - Label 'Hierarchy identifier'\n", + "Entity 'http://edamontology.org/data_2591' - Label 'Brite hierarchy ID'\n", + "Entity 'http://edamontology.org/data_2591' - Label 'Brite hierarchy ID'\n", + "Entity 'http://edamontology.org/data_2592' - Label 'Cancer type'\n", + "Entity 'http://edamontology.org/data_2592' - Label 'Cancer type'\n", + "Entity 'http://edamontology.org/data_2593' - Label 'BRENDA organism ID'\n", + "Entity 'http://edamontology.org/data_2593' - Label 'BRENDA organism ID'\n", + "Entity 'http://edamontology.org/data_2594' - Label 'UniGene taxon'\n", + "Entity 'http://edamontology.org/data_2595' - Label 'UTRdb taxon'\n", + "Entity 'http://edamontology.org/data_2596' - Label 'Catalogue ID'\n", + "Entity 'http://edamontology.org/data_2597' - Label 'CABRI catalogue name'\n", + "Entity 'http://edamontology.org/data_2597' - Label 'CABRI catalogue name'\n", + "Entity 'http://edamontology.org/data_2598' - Label 'Secondary structure alignment metadata'\n", + "Entity 'http://edamontology.org/data_2598' - Label 'Secondary structure alignment metadata'\n", + "Entity 'http://edamontology.org/data_2599' - Label 'Molecule interaction report'\n", + "Entity 'http://edamontology.org/data_2599' - Label 'Molecule interaction report'\n", + "Entity 'http://edamontology.org/data_2600' - Label 'Pathway or network'\n", + "Entity 'http://edamontology.org/data_2600' - Label 'Pathway or network'\n", + "Entity 'http://edamontology.org/data_2601' - Label 'Small molecule data'\n", + "Entity 'http://edamontology.org/data_2601' - Label 'Small molecule data'\n", + "Entity 'http://edamontology.org/data_2602' - Label 'Genotype and phenotype data'\n", + "Entity 'http://edamontology.org/data_2602' - Label 'Genotype and phenotype data'\n", + "Entity 'http://edamontology.org/data_2603' - Label 'Expression data'\n", + "Entity 'http://edamontology.org/data_2603' - Label 'Expression data'\n", + "Entity 'http://edamontology.org/data_2605' - Label 'Compound ID (KEGG)'\n", + "Entity 'http://edamontology.org/data_2605' - Label 'Compound ID (KEGG)'\n", + "Entity 'http://edamontology.org/data_2606' - Label 'RFAM name'\n", + "Entity 'http://edamontology.org/data_2606' - Label 'RFAM name'\n", + "Entity 'http://edamontology.org/data_2608' - Label 'Reaction ID (KEGG)'\n", + "Entity 'http://edamontology.org/data_2608' - Label 'Reaction ID (KEGG)'\n", + "Entity 'http://edamontology.org/data_2609' - Label 'Drug ID (KEGG)'\n", + "Entity 'http://edamontology.org/data_2609' - Label 'Drug ID (KEGG)'\n", + "Entity 'http://edamontology.org/data_2609' - Label 'Drug ID (KEGG)'\n", + "Entity 'http://edamontology.org/data_2610' - Label 'Ensembl ID'\n", + "Entity 'http://edamontology.org/data_2610' - Label 'Ensembl ID'\n", + "Entity 'http://edamontology.org/data_2611' - Label 'ICD identifier'\n", + "Entity 'http://edamontology.org/data_2611' - Label 'ICD identifier'\n", + "Entity 'http://edamontology.org/data_2611' - Label 'ICD identifier'\n", + "Entity 'http://edamontology.org/data_2612' - Label 'Sequence cluster ID (CluSTr)'\n", + "Entity 'http://edamontology.org/data_2612' - Label 'Sequence cluster ID (CluSTr)'\n", + "Entity 'http://edamontology.org/data_2613' - Label 'KEGG Glycan ID'\n", + "Entity 'http://edamontology.org/data_2613' - Label 'KEGG Glycan ID'\n", + "Entity 'http://edamontology.org/data_2613' - Label 'KEGG Glycan ID'\n", + "Entity 'http://edamontology.org/data_2614' - Label 'TCDB ID'\n", + "Entity 'http://edamontology.org/data_2614' - Label 'TCDB ID'\n", + "Entity 'http://edamontology.org/data_2615' - Label 'MINT ID'\n", + "Entity 'http://edamontology.org/data_2615' - Label 'MINT ID'\n", + "Entity 'http://edamontology.org/data_2616' - Label 'DIP ID'\n", + "Entity 'http://edamontology.org/data_2616' - Label 'DIP ID'\n", + "Entity 'http://edamontology.org/data_2617' - Label 'Signaling Gateway protein ID'\n", + "Entity 'http://edamontology.org/data_2617' - Label 'Signaling Gateway protein ID'\n", + "Entity 'http://edamontology.org/data_2618' - Label 'Protein modification ID'\n", + "Entity 'http://edamontology.org/data_2619' - Label 'RESID ID'\n", + "Entity 'http://edamontology.org/data_2619' - Label 'RESID ID'\n", + "Entity 'http://edamontology.org/data_2620' - Label 'RGD ID'\n", + "Entity 'http://edamontology.org/data_2620' - Label 'RGD ID'\n", + "Entity 'http://edamontology.org/data_2621' - Label 'TAIR accession (protein)'\n", + "Entity 'http://edamontology.org/data_2621' - Label 'TAIR accession (protein)'\n", + "Entity 'http://edamontology.org/data_2622' - Label 'Compound ID (HMDB)'\n", + "Entity 'http://edamontology.org/data_2622' - Label 'Compound ID (HMDB)'\n", + "Entity 'http://edamontology.org/data_2625' - Label 'LIPID MAPS ID'\n", + "Entity 'http://edamontology.org/data_2625' - Label 'LIPID MAPS ID'\n", + "Entity 'http://edamontology.org/data_2626' - Label 'PeptideAtlas ID'\n", + "Entity 'http://edamontology.org/data_2626' - Label 'PeptideAtlas ID'\n", + "Entity 'http://edamontology.org/data_2627' - Label 'Molecular interaction ID'\n", + "Entity 'http://edamontology.org/data_2627' - Label 'Molecular interaction ID'\n", + "Entity 'http://edamontology.org/data_2628' - Label 'BioGRID interaction ID'\n", + "Entity 'http://edamontology.org/data_2628' - Label 'BioGRID interaction ID'\n", + "Entity 'http://edamontology.org/data_2629' - Label 'Enzyme ID (MEROPS)'\n", + "Entity 'http://edamontology.org/data_2629' - Label 'Enzyme ID (MEROPS)'\n", + "Entity 'http://edamontology.org/data_2630' - Label 'Mobile genetic element ID'\n", + "Entity 'http://edamontology.org/data_2631' - Label 'ACLAME ID'\n", + "Entity 'http://edamontology.org/data_2631' - Label 'ACLAME ID'\n", + "Entity 'http://edamontology.org/data_2632' - Label 'SGD ID'\n", + "Entity 'http://edamontology.org/data_2632' - Label 'SGD ID'\n", + "Entity 'http://edamontology.org/data_2633' - Label 'Book ID'\n", + "Entity 'http://edamontology.org/data_2634' - Label 'ISBN'\n", + "Entity 'http://edamontology.org/data_2634' - Label 'ISBN'\n", + "Entity 'http://edamontology.org/data_2635' - Label 'Compound ID (3DMET)'\n", + "Entity 'http://edamontology.org/data_2635' - Label 'Compound ID (3DMET)'\n", + "Entity 'http://edamontology.org/data_2636' - Label 'MatrixDB interaction ID'\n", + "Entity 'http://edamontology.org/data_2636' - Label 'MatrixDB interaction ID'\n", + "Entity 'http://edamontology.org/data_2637' - Label 'cPath ID'\n", + "Entity 'http://edamontology.org/data_2637' - Label 'cPath ID'\n", + "Entity 'http://edamontology.org/data_2637' - Label 'cPath ID'\n", + "Entity 'http://edamontology.org/data_2638' - Label 'PubChem bioassay ID'\n", + "Entity 'http://edamontology.org/data_2638' - Label 'PubChem bioassay ID'\n", + "Entity 'http://edamontology.org/data_2639' - Label 'PubChem ID'\n", + "Entity 'http://edamontology.org/data_2639' - Label 'PubChem ID'\n", + "Entity 'http://edamontology.org/data_2641' - Label 'Reaction ID (MACie)'\n", + "Entity 'http://edamontology.org/data_2641' - Label 'Reaction ID (MACie)'\n", + "Entity 'http://edamontology.org/data_2642' - Label 'Gene ID (miRBase)'\n", + "Entity 'http://edamontology.org/data_2642' - Label 'Gene ID (miRBase)'\n", + "Entity 'http://edamontology.org/data_2643' - Label 'Gene ID (ZFIN)'\n", + "Entity 'http://edamontology.org/data_2643' - Label 'Gene ID (ZFIN)'\n", + "Entity 'http://edamontology.org/data_2644' - Label 'Reaction ID (Rhea)'\n", + "Entity 'http://edamontology.org/data_2644' - Label 'Reaction ID (Rhea)'\n", + "Entity 'http://edamontology.org/data_2645' - Label 'Pathway ID (Unipathway)'\n", + "Entity 'http://edamontology.org/data_2645' - Label 'Pathway ID (Unipathway)'\n", + "Entity 'http://edamontology.org/data_2646' - Label 'Compound ID (ChEMBL)'\n", + "Entity 'http://edamontology.org/data_2646' - Label 'Compound ID (ChEMBL)'\n", + "Entity 'http://edamontology.org/data_2647' - Label 'LGICdb identifier'\n", + "Entity 'http://edamontology.org/data_2647' - Label 'LGICdb identifier'\n", + "Entity 'http://edamontology.org/data_2648' - Label 'Reaction kinetics ID (SABIO-RK)'\n", + "Entity 'http://edamontology.org/data_2649' - Label 'PharmGKB ID'\n", + "Entity 'http://edamontology.org/data_2649' - Label 'PharmGKB ID'\n", + "Entity 'http://edamontology.org/data_2650' - Label 'Pathway ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2650' - Label 'Pathway ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2650' - Label 'Pathway ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2651' - Label 'Disease ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2651' - Label 'Disease ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2651' - Label 'Disease ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2652' - Label 'Drug ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2652' - Label 'Drug ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2652' - Label 'Drug ID (PharmGKB)'\n", + "Entity 'http://edamontology.org/data_2653' - Label 'Drug ID (TTD)'\n", + "Entity 'http://edamontology.org/data_2653' - Label 'Drug ID (TTD)'\n", + "Entity 'http://edamontology.org/data_2654' - Label 'Target ID (TTD)'\n", + "Entity 'http://edamontology.org/data_2654' - Label 'Target ID (TTD)'\n", + "Entity 'http://edamontology.org/data_2655' - Label 'Cell type identifier'\n", + "Entity 'http://edamontology.org/data_2656' - Label 'NeuronDB ID'\n", + "Entity 'http://edamontology.org/data_2656' - Label 'NeuronDB ID'\n", + "Entity 'http://edamontology.org/data_2657' - Label 'NeuroMorpho ID'\n", + "Entity 'http://edamontology.org/data_2657' - Label 'NeuroMorpho ID'\n", + "Entity 'http://edamontology.org/data_2658' - Label 'Compound ID (ChemIDplus)'\n", + "Entity 'http://edamontology.org/data_2658' - Label 'Compound ID (ChemIDplus)'\n", + "Entity 'http://edamontology.org/data_2659' - Label 'Pathway ID (SMPDB)'\n", + "Entity 'http://edamontology.org/data_2659' - Label 'Pathway ID (SMPDB)'\n", + "Entity 'http://edamontology.org/data_2660' - Label 'BioNumbers ID'\n", + "Entity 'http://edamontology.org/data_2662' - Label 'T3DB ID'\n", + "Entity 'http://edamontology.org/data_2662' - Label 'T3DB ID'\n", + "Entity 'http://edamontology.org/data_2663' - Label 'Carbohydrate identifier'\n", + "Entity 'http://edamontology.org/data_2663' - Label 'Carbohydrate identifier'\n", + "Entity 'http://edamontology.org/data_2663' - Label 'Carbohydrate identifier'\n", + "Entity 'http://edamontology.org/data_2664' - Label 'GlycomeDB ID'\n", + "Entity 'http://edamontology.org/data_2664' - Label 'GlycomeDB ID'\n", + "Entity 'http://edamontology.org/data_2665' - Label 'LipidBank ID'\n", + "Entity 'http://edamontology.org/data_2665' - Label 'LipidBank ID'\n", + "Entity 'http://edamontology.org/data_2666' - Label 'CDD ID'\n", + "Entity 'http://edamontology.org/data_2666' - Label 'CDD ID'\n", + "Entity 'http://edamontology.org/data_2667' - Label 'MMDB ID'\n", + "Entity 'http://edamontology.org/data_2667' - Label 'MMDB ID'\n", + "Entity 'http://edamontology.org/data_2668' - Label 'iRefIndex ID'\n", + "Entity 'http://edamontology.org/data_2668' - Label 'iRefIndex ID'\n", + "Entity 'http://edamontology.org/data_2669' - Label 'ModelDB ID'\n", + "Entity 'http://edamontology.org/data_2669' - Label 'ModelDB ID'\n", + "Entity 'http://edamontology.org/data_2670' - Label 'Pathway ID (DQCS)'\n", + "Entity 'http://edamontology.org/data_2670' - Label 'Pathway ID (DQCS)'\n", + "Entity 'http://edamontology.org/data_2671' - Label 'Ensembl ID (Homo sapiens)'\n", + "Entity 'http://edamontology.org/data_2671' - Label 'Ensembl ID (Homo sapiens)'\n", + "Entity 'http://edamontology.org/data_2672' - Label 'Ensembl ID ('Bos taurus')'\n", + "Entity 'http://edamontology.org/data_2672' - Label 'Ensembl ID ('Bos taurus')'\n", + "Entity 'http://edamontology.org/data_2673' - Label 'Ensembl ID ('Canis familiaris')'\n", + "Entity 'http://edamontology.org/data_2673' - Label 'Ensembl ID ('Canis familiaris')'\n", + "Entity 'http://edamontology.org/data_2674' - Label 'Ensembl ID ('Cavia porcellus')'\n", + "Entity 'http://edamontology.org/data_2674' - Label 'Ensembl ID ('Cavia porcellus')'\n", + "Entity 'http://edamontology.org/data_2675' - Label 'Ensembl ID ('Ciona intestinalis')'\n", + "Entity 'http://edamontology.org/data_2675' - Label 'Ensembl ID ('Ciona intestinalis')'\n", + "Entity 'http://edamontology.org/data_2676' - Label 'Ensembl ID ('Ciona savignyi')'\n", + "Entity 'http://edamontology.org/data_2676' - Label 'Ensembl ID ('Ciona savignyi')'\n", + "Entity 'http://edamontology.org/data_2677' - Label 'Ensembl ID ('Danio rerio')'\n", + "Entity 'http://edamontology.org/data_2677' - Label 'Ensembl ID ('Danio rerio')'\n", + "Entity 'http://edamontology.org/data_2678' - Label 'Ensembl ID ('Dasypus novemcinctus')'\n", + "Entity 'http://edamontology.org/data_2678' - Label 'Ensembl ID ('Dasypus novemcinctus')'\n", + "Entity 'http://edamontology.org/data_2679' - Label 'Ensembl ID ('Echinops telfairi')'\n", + "Entity 'http://edamontology.org/data_2679' - Label 'Ensembl ID ('Echinops telfairi')'\n", + "Entity 'http://edamontology.org/data_2680' - Label 'Ensembl ID ('Erinaceus europaeus')'\n", + "Entity 'http://edamontology.org/data_2680' - Label 'Ensembl ID ('Erinaceus europaeus')'\n", + "Entity 'http://edamontology.org/data_2681' - Label 'Ensembl ID ('Felis catus')'\n", + "Entity 'http://edamontology.org/data_2681' - Label 'Ensembl ID ('Felis catus')'\n", + "Entity 'http://edamontology.org/data_2682' - Label 'Ensembl ID ('Gallus gallus')'\n", + "Entity 'http://edamontology.org/data_2682' - Label 'Ensembl ID ('Gallus gallus')'\n", + "Entity 'http://edamontology.org/data_2683' - Label 'Ensembl ID ('Gasterosteus aculeatus')'\n", + "Entity 'http://edamontology.org/data_2683' - Label 'Ensembl ID ('Gasterosteus aculeatus')'\n", + "Entity 'http://edamontology.org/data_2684' - Label 'Ensembl ID ('Homo sapiens')'\n", + "Entity 'http://edamontology.org/data_2684' - Label 'Ensembl ID ('Homo sapiens')'\n", + "Entity 'http://edamontology.org/data_2685' - Label 'Ensembl ID ('Loxodonta africana')'\n", + "Entity 'http://edamontology.org/data_2685' - Label 'Ensembl ID ('Loxodonta africana')'\n", + "Entity 'http://edamontology.org/data_2686' - Label 'Ensembl ID ('Macaca mulatta')'\n", + "Entity 'http://edamontology.org/data_2686' - Label 'Ensembl ID ('Macaca mulatta')'\n", + "Entity 'http://edamontology.org/data_2687' - Label 'Ensembl ID ('Monodelphis domestica')'\n", + "Entity 'http://edamontology.org/data_2687' - Label 'Ensembl ID ('Monodelphis domestica')'\n", + "Entity 'http://edamontology.org/data_2688' - Label 'Ensembl ID ('Mus musculus')'\n", + "Entity 'http://edamontology.org/data_2688' - Label 'Ensembl ID ('Mus musculus')'\n", + "Entity 'http://edamontology.org/data_2689' - Label 'Ensembl ID ('Myotis lucifugus')'\n", + "Entity 'http://edamontology.org/data_2689' - Label 'Ensembl ID ('Myotis lucifugus')'\n", + "Entity 'http://edamontology.org/data_2690' - Label 'Ensembl ID (\"Ornithorhynchus anatinus\")'\n", + "Entity 'http://edamontology.org/data_2690' - Label 'Ensembl ID (\"Ornithorhynchus anatinus\")'\n", + "Entity 'http://edamontology.org/data_2691' - Label 'Ensembl ID ('Oryctolagus cuniculus')'\n", + "Entity 'http://edamontology.org/data_2691' - Label 'Ensembl ID ('Oryctolagus cuniculus')'\n", + "Entity 'http://edamontology.org/data_2692' - Label 'Ensembl ID ('Oryzias latipes')'\n", + "Entity 'http://edamontology.org/data_2692' - Label 'Ensembl ID ('Oryzias latipes')'\n", + "Entity 'http://edamontology.org/data_2693' - Label 'Ensembl ID ('Otolemur garnettii')'\n", + "Entity 'http://edamontology.org/data_2693' - Label 'Ensembl ID ('Otolemur garnettii')'\n", + "Entity 'http://edamontology.org/data_2694' - Label 'Ensembl ID ('Pan troglodytes')'\n", + "Entity 'http://edamontology.org/data_2694' - Label 'Ensembl ID ('Pan troglodytes')'\n", + "Entity 'http://edamontology.org/data_2695' - Label 'Ensembl ID ('Rattus norvegicus')'\n", + "Entity 'http://edamontology.org/data_2695' - 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