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cv_data_releases.txt
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----------------------------------------------------------------------------
This document lists the controlled vocabulary used to defined imported data
(cv_data_release) in neXtProt database
Release: 25-Oct-2019
The definition of the CV is provided in the following format:
----------- ---------------------------------- -----------------------------
Line code Content Occurrence in an entry
----------- ---------------------------------- -----------------------------
ID Unique identifier Once; starts a cv data release entry
AC Unique accession (CVDR-xxxx) Once
DE Definition Once or more
DS Datasource of the downloaded data Once
DR Data repository / ftp site where the Once
data are downloadable
UF Data update frequency Once
UR Data internet site url Once
CI Contact information Once or more
// Terminator Once; ends an entry
next id: CVDR-0310
__________________________________________________________________________
ID Additional references
AC CVDR-0033
DE Publications: Additional computationally mapped publications
DS PIR
DR freud.isb-sib.ch:/share/sib/sp/data/medline/pir_mapping.tab
UF monthly, linked to uniprot update
UR
CI
//
ID Antibodypedia
AC CVDR-0084
DE Identifiers: antibodies against human proteins.
DS Antibodypedia
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/identifiers/antibodypedia.log
UF monthly
UR
CI
//
ID Bioeditor
AC CVDR-0098
DE Annotations: annotation manually created by neXtProt via the Bioeditor platform.
DS Bioeditor
UF occasionally
UR
CI
//
ID BGee
AC CVDR-0035
DE Data: expression data based on microarray and EST
DS Bgee
DR ftp://lausanne.isb-sib.ch/pub/databases/Bgee/external_data/neXtProtBgeeData.zip
UF twice a year
UR http://bgee.unil.ch
CI
//
ID CCDS
AC CVDR-0039
DE Identifiers: Protein cross references on CCDS
DS CCDS
DR gefiles.isb-sib.ch:/work/Swiss-Prot/outgoing/nextprot/ccds
UF monthly, linked to uniprot update
UR
CI
//
ID Clinvar
AC CVDR-0087
DE Data: Gene variant annotations
DE Database of mutations and their clinical relevance
DS Clinvar
DR ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_00-latest.xml.gz
UF occasionally
UR http://www.ncbi.nlm.nih.gov/clinvar/
CI
//
ID Cosmic
AC CVDR-0065
DE Data: Gene variant annotations
DE Catalogue Of Somatic Mutations In Cancer
DS Cosmic
DR ftp.sanger.ac.uk/pub/CGP/cosmic/data_export/CosmicMutantExport_*.tsv.gz
UF occasionally
UR http://www.sanger.ac.uk/genetics/CGP/cosmic/
CI
//
ID Databases
AC CVDR-0023
DE Control vocabulary, list of databases used in bioinformatics
DS Uniprot
DR gefiles.isb-sib.ch:/work/grp-sprot/sptr/current_release/dbxref.txt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/more-dbxrefs.txt
UF monthly
UR http://www.uniprot.org/docs/#general
CI
//
ID Dyp
AC CVDR-0047
DE Data: Subcellular location annotation.
DE The Kahn Dynamic Proteomics project aims at monitoring the position and amounts of endogenous
DE proteins in individual living human cells.
DS Dyp
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/annotations/DYP.xml
UF
UR http://www.weizmann.ac.il/mcb/UriAlon/DynamProt/index.html
CI
//
ID ECO
AC CVDR-0064
DE Ontology: A rich ontology for experimental and other evidence statements.
DS OBO
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_sequence_ontology.txt
UF when needed (new data to load)
UR http://www.sequenceontology.org/
CI
//
ID EMBL names
AC CVDR-0030
DE Identifiers: Clone names
DS EMBL-EBI
DR http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBL&format=emblxml
UF rarely
UR
CI
//
ID Ensembl genome
AC CVDR-0025
DE Data: Genes, transcripts and exons
DS Ensembl
DR ftp.ensembl.org/pub/release-$ENSEMBL_VERSION/mysql/homo_sapiens_core_$ENSEMBL_VERSION_LONG
UF every two months
UR http://www.ensembl.org/
CI
//
ID Ensembl names
AC CVDR-0031
DE Identifiers: Probe and probeset names
DS Ensembl
DR ftp.ensembl.org/pub/release-$ENSEMBL_VERSION/mysql/homo_sapiens_funcgen_$ENSEMBL_VERSION_LONG
UF rarely
UR
CI
//
ID Ensembl variants
AC CVDR-0029
DE Data: Gene variant annotations
DS Ensembl
DR ftp.ensembl.org/pub/release-$ENSEMBL_VERSION/mysql/homo_sapiens_variation_$ENSEMBL_VERSION_LONG
UF every two months
UR http://www.ensembl.org/
CI
//
ID eVOC
AC CVDR-0020
DE Ontology: anatomical system, developmental stage and pathology ontologies
DS eVOC
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/anatomicalsystem.obo
DR freud.isb-sib.ch:/.../cv/celltype.obo
DR freud.isb-sib.ch:/.../cv/developmentstage.obo
DR freud.isb-sib.ch:/.../cv/pathology.obo
UF never, obsolete
UR
CI
//
ID GeneId
AC CVDR-0041
DE Identifiers: Gene ids from NCBI
DS NCBI
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/identifiers/geneid.log
UF once
UR
CI
//
ID GFP-cDNA@EMBL
AC CVDR-0043
DE Data: GFP-cDNA subcellular location annotations
DS GFP-cDNA@EMBL
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/annotations/GFP_cDNA.xml
UF once
UR http://gfp-cdna.embl.de/
CI
//
ID GlyConnect
AC CVDR-0151
DE Proteomics data (PTM) extracted from PubMed publications.
DE Glycosylation identified by mass spectrometry.
DS GlyConnect
UF twice a year
UR https://glyconnect.expasy.org/
CI
//
ID gnomAD
AC CVDR-0156
DE Genome Aggregation Database
DS gnomAD
UF once a year
UR https://gnomad.broadinstitute.org/
CI
//
ID GO
AC CVDR-0001
DE Ontology: Gene Ontology
DS GO
DR http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo
UF monthly, linked to uniprot update
UR http://www.geneontology.org/
CI
//
ID GO annotations
AC CVDR-0027
DE Data: Gene Ontology annotations
DS GO
DR ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz
UF monthly, linked to uniprot update
UR http://www.ebi.ac.uk/GOA
CI
//
ID HPA
AC CVDR-0034
DE Data: expression data based on immunohistochemisty; Subcellular location data based on immunofluorescently stained cell
DS Human protein atlas
DR https://docs.google.com/open?id=xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
DR http://www.proteinatlas.org/download/proteinatlas.xml.zip
UF twice a year
UR http://www.proteinatlas.org/
CI
//
ID HPRD
AC CVDR-0038
DE Identifiers: Protein cross references on HPRD
DS HPRD
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/identifiers/hprd.log
UF once
UR
CI
//
ID Human PeptideAtlas
AC CVDR-0061
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human samples, load of accession codes only.
DS PeptideAtlas
DR http://www.peptideatlas.org/builds/human/201207/APD_Hs_all.fasta
UF rarely
UR http://www.peptideatlas.org
CI
//
ID Human Phosphoproteome PeptideAtlas
AC CVDR-0091
DE Proteomics data (peptides + PTM): Integration of peptide sequences and PTM obtained by high-throughput mass spectrometry.
DE Peptides and phosphorylations identified by mass spectrometry.
DS PeptideAtlas human phosphoproteome
DR ftp://ftp.peptideatlas.org/Phospho/peptide_ptm.xls.gz
UF rarely
UR http://www.peptideatlas.org
CI
//
ID Human SRMAtlas
AC CVDR-0089
DE Proteomics data (peptides): Compendium of targeted proteomics assays to detect and quantify proteins in
DE complex proteome digests by mass spectrometry.
DS SRMAtlas
DR https://db.systemsbiology.net//sbeams/cgi/PeptideAtlas/GetPeptides?QUERY_NAME=AT_GetPeptides;action=QUERY;output_mode=tsv;SBEAMSentrycode=SRMATLASPREVIEW;organism_specialized_build=Human Synthetic
UF rarely
UR http://www.srmatlas.org
CI
//
ID ICEPO
AC CVDR-0097
DE Control vocabulary for electrophysiological properties of ion channels.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/bioeditor/_tech_docs/icepo.obo
UF occasionally
UR
CI
//
ID IntAct interactions
AC CVDR-0028
DE Data: Protein interaction data
DS EMBL-EBI
DR ftp.ebi.ac.uk/pub/databases/intact/current/various/uniprotcomments.dat
UF monthly, linked to uniprot update
UR
CI
//
ID InterPro
AC CVDR-0037
DE Documents: InterPro documents referenced in neXtProt entries
DS InterPro
DR ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz
UF monthly, linked to uniprot update
UR http://www.ebi.ac.uk/interpro/
CI
//
ID IPI
AC CVDR-0083
DE Identifiers: Entrez Gene symbol
DS NCBI
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/identifiers/IPI.log
UF once
UR
CI
//
ID KEGGPathway
AC CVDR-0049
DE Identifiers: KEGG Pathway is a collection of manually drawn pathway maps.
DS KEGG_PTW
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/identifiers/kegg-pathways.txt
UF once
UR http://www.genome.jp/kegg/pathway.html
CI
//
ID LOC
AC CVDR-0040
DE Identifiers: Locus names from NCBI
DS NCBI
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/identifiers/loc.log
UF once
UR
CI
//
ID Mammalian Phenotype
AC CVDR-0095
DE Control vocabulary for mammalian phenotype.
DS MGI
DR ftp://ftp.informatics.jax.org/pub/reports/HOM_MouseHumanSequence.rpt
UF monthly, linked to bioeditor annotations update
UR
CI
//
ID MDATA_0004_2011
AC CVDR-0048
DE Proteomics data (peptides) extracted from direct submission
DE Mitochondria-enriched N-terminome and proteome of myelomonocytic histiocytic lymphoma cell.
DE Direct submission of proteomics data.
DS MDATA_0004_2011
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/MDATA_0004_2011.xml
UF once
UR
CI
//
ID MDATA_0023_2012
AC CVDR-0068
DE Proteomics data (peptides) extracted from direct submission.
DE Human pancreatic islets proteome
DE Direct submission of proteomics data.
DS MDATA_0023_2012
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/MDATA_0023_2012.xml
UF once
UR
CI
//
ID MDATA_0033_2013
AC CVDR-0077
DE Proteomics data (peptides) extracted from direct submission.
DE Peptides in substantia nigra tissue.
DE Direct submission of proteomics data.
DS MDATA_0033_2013
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/MDATA_0033_2013.xml
UF once
UR
CI
//
ID MeSH
AC CVDR-0002
DE Ontology: Medical Subject Headings
DS MeSH
DR ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/xmlmesh/desc*.xml
UF yearly
UR http://www.nlm.nih.gov/mesh/MBrowser.html
CI
//
ID MetaData
AC CVDR-0042
DE Document: description of a data set
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/metadata_files/metadata.txt
UF occasionally
UR
CI
//
ID MGI
AC CVDR-0050
DE Identifiers: MGI is the international database resource for the laboratory mouse, providing integrated genetic,
DE genomic, and biological data to facilitate the study of human health and disease.
DS MGI
DR ftp.informatics.jax.org/pub/reports/HMD_HGNC_Accession.rpt
UF monthly, linked to uniprot update
UR http://www.informatics.jax.org/
CI
//
ID NCI Metathesaurus
AC CVDR-0088
DE Ontology: Wide-ranging biomedical terminology database.
DE It covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities.
DE Needs an UMLS account (login = nextprot, password: cf template load)
DS NCI
DR https://cbiit.nci.nih.gov/evs-download/index/metathesaurus-downloads/metval/Metathesaurus.RRF.zip
UF when needed (new data to load)
UR http://ncimeta.nci.nih.gov/
CI
//
ID NCI Thesaurus
AC CVDR-0085
DE Ontology: Reference terminology for many NCI and other systems.
DE It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities
DS NCI
DR http://evs.nci.nih.gov/ftp1/NCI_Thesaurus/Thesaurus_YY.MMx.OWL.zip
UF when needed (new data to load)
UR http://ncit.nci.nih.gov/
CI
//
ID neXtProt annotation category
AC CVDR-0003
DE Control vocabulary for annotations categories
DS NEXTPROT
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_annotations.txt
UF rarely
UR
CI
//
ID neXtProt cell line
AC CVDR-0006
DE Control vocabulary for cell lines.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_cell_line.txt
UF occasionally
UR
CI
//
ID neXtProt datasources
AC CVDR-0062
DE Control vocabulary: document that describes datasources
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_datasources.txt
UF when needed (new data to load)
UR
CI
//
ID neXtProt developmental stage
AC CVDR-0005
DE Ontology for developmental and metastage
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/developmental_stage.txt
UF occasionally, linked to expression data update
UR
CI
//
ID neXtProt family
AC CVDR-0004
DE Control vocabulary for the protein families
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_family.txt
UF monthly, linked to uniprot update
UR
CI
//
ID neXtProt modification effect
AC CVDR-0096
DE Control vocabulary for the modification effect
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/bioeditor/_tech_docs/be_tech_note_18_modification_effect.obo
UF monthly, linked to bioeditor annotations update
UR
CI
//
ID neXtProt protein property
AC CVDR-0094
DE Control vocabulary for the protein properties
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/bioeditor/_tech_docs/be_tech_note_17_protein_property.obo
UF monthly, linked to bioeditor annotations update
UR
CI
//
ID neXtProt tissue
AC CVDR-0007
DE Ontology for anatomical system.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/caloha.obo
UF occasionally, linked to expression data update
UR
CI
//
ID Non-standard amino acid
AC CVDR-0008
DE Control vocabulary for non-standard residues.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_non_std_amino_acids.txt
UF occasionally
UR
CI
//
ID PMID_18614565
AC CVDR-0059
DE Proteomics data (peptides) extracted from PubMed publication.
DE Proteome
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/18614565.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=18614565
CI
//
ID PMID_19413330
AC CVDR-0082
DE Proteomics data (PTM) extracted from PubMed publication.
DE Peptides and phosphorylation sites in HEK293 cells.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/19413330.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=19413330
CI
//
ID PMID_19608861
AC CVDR-0057
DE Proteomics data (PTM) extracted from PubMed publication.
DE Lysine-Acetylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/19608861.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=19608861
CI
//
ID PMID_20068231
AC CVDR-0051
DE Proteomics data (PTM) extracted from PubMed publication.
DE Phosphorylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/20068231.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=20068231
CI
//
ID PMID_20140087
AC CVDR-0054
DE Proteomics data (PTM) extracted from PubMed publication.
DE S-Nitrosylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/20140087.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=20140087
CI
//
ID PMID_20570859
AC CVDR-0045
DE Proteomics data (PTM) extracted from PubMed publication.
DE Glycosylation of cell surface proteins in myeloid leukemia cell lines.
DE Glycosylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/20570859.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=20570859
CI
//
ID PMID_20687582
AC CVDR-0056
DE Proteomics data (PTM) extracted from PubMed publication.
DE S-Nitrosylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/20687582.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=20687582
CI
//
ID PMID_20797634
AC CVDR-0055
DE Proteomics data (PTM) extracted from PubMed publication.
DE Sumoylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/20797634.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=
CI
//
ID PMID_20972266
AC CVDR-0052
DE Proteomics data (PTM) extracted from PubMed publication.
DE Ubiquitylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/20972266.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=20972266
CI
//
ID PMID_21139048
AC CVDR-0053
DE Proteomics data (PTM) extracted from PubMed publication.
DE Ubiquitylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/21139048.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=21139048
CI
//
ID PMID_21406692
AC CVDR-0046
DE Proteomics data (PTM) extracted from PubMed publication.
DE Identification, phosphorylation and N-acetylation of embryonic stem cells proteins.
DE Phosphorylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/21406692.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=21406692
CI
//
ID PMID_21645671
AC CVDR-0058
DE Proteomics data (PTM) extracted from PubMed publication.
DE Glycosylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/21645671.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=21645671
CI
//
ID PMID_21890473
AC CVDR-0081
DE Proteomics data (PTM) extracted from PubMed publication.
DE Lysine ubiquitination sites in MV4-11 and HEK293T cells.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/21890473.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=21890473
CI
//
ID PMID_22148984
AC CVDR-0069
DE Proteomics data (PTM) extracted from PubMed publication.
DE Glycosylation of whole cell proteins in human pancreatic islets.
DE Glycosylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/22148984.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=22148984
CI
//
ID PMID_22199227
AC CVDR-0070
DE Proteomics data (PTM) extracted from PubMed publication.
DE Phosphorylation sites in telomerase-expressing human retinal epithelial
DE (hTERT-RPE) cells.
DE Phosphorylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/22199227.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=22199227
CI
//
ID PMID_22468782
AC CVDR-0071
DE Proteomics data (PTM) extracted from PubMed publication.
DE Phosphorylation sites in HeLa cells.
DE Phosphorylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/22468782.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=22468782
CI
//
ID PMID_22865923
AC CVDR-0072
DE Proteomics data (PTM) extracted from PubMed publication.
DE Arginine and lysine methylation sites.
DE Methylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/22865923.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=22865923
CI
//
ID PMID_23153008
AC CVDR-0075
DE Proteomics data (peptides) extracted from PubMed publication.
DE Peptides in breast cancer tissues.
DE Peptides identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/23153008.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=23153008
CI
//
ID PMID_23236377
AC CVDR-0080
DE Proteomics data (PTM) extracted from PubMed publication.
DE Lysine acetylation sites in human U2OS cells.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/23236377.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=23236377
CI
//
ID PMID_23266961
AC CVDR-0076
DE Proteomics data (PTM) extracted from PubMed publication.
DE Lysine ubiquitination and N-acetylation sites in Jurkat E6.1 cells.
DE Ubiquitination and N-acetylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/23266961.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=23266961
CI
//
ID PMID_23312004
AC CVDR-0073
DE Proteomics data (PTM) extracted from PubMed publication.
DE Peptides and phosphorylation sites from colorectal cancer and normal tissue and cell lines.
DE Phosphorylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/23312004.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=23312004
CI
//
ID PMID_23584533
AC CVDR-0074
DE Proteomics data (PTM) extracted from PubMed publication.
DE Human cellular O-GalNAc glycoproteome.
DE Glycosylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/23584533.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=23584533
CI
//
ID PMID_23955771
AC CVDR-0092
DE Proteomics data (PTM) extracted from PubMed publication.
DE Asp- and Glu-ADP-ribosylation in human colorectal carcinoma cells.
DE ADP-ribosylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/23955771.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=23955771
CI
//
ID PMID_24129315
AC CVDR-0086
DE Proteomics data (PTM) extracted from PubMed publication.
DE Lysine and arginine methylation sites in human HCT116 cells.
DE Methylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/24129315.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=24129315
CI
//
ID PMID_25038526
AC CVDR-0093
DE Proteomics data (PTM) extracted from PubMed publication.
DE Lys-acetylation in human capacitated sperm.
DE Acetylation identified by mass spectrometry.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/25038526.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=25038526
CI
//
ID PMID_25218447
AC CVDR-0090
DE Proteomics data (PTM) extracted from PubMed publication.
DE Global sumoylation in HeLa cells.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/XML/proteomics/25218447.xml
UF once
UR http://www.ncbi.nlm.nih.gov/pubmed?term=25218447
CI
//
ID PROSITEDOC
AC CVDR-0036
DE Documents: Prosite documents referenced in neXtProt entries
DS Prosite
DR ftp.expasy.org/databases/prosite/prosite.doc
UF monthly, linked to uniprot update
UR http://www.expasy.org/prosite/
CI
//
ID PubMed journal
AC CVDR-0024
DE Control vocabulary, list of journals and their official abbreviation
DS PubMed
DR ftp://ftp.ncbi.nih.gov/pubmed/J_Entrez.txt
UF monthly, linked to uniprot update
UR
CI
//
ID PubMed publications
AC CVDR-0032
DE Publications
DS PubMed
DR http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=xml
UF monthly, linked to uniprot update
UR http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed
CI
//
ID Sequence ontology
AC CVDR-0063
DE Ontology: the Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_sequence_ontology.txt
UF when needed (new data to load)
UR http://www.sequenceontology.org/
CI
//
ID UniProtKB
AC CVDR-0026
DE Data: Protein sequence and annotation data
DS Uniprot
DR gefiles.isb-sib.ch:/work/Swiss-Prot/outgoing/nextprot/uniprot_sprot.xml.gz
UF monthly
UR http://www.uniprot.org/
CI
//
ID UniProtKB carbohydrate
AC CVDR-0009
DE Control vocabulary for carbohydrates added to proteins.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_carbohydrate.txt
UF occasionally
UR
CI
//
ID UniProtKB disease
AC CVDR-0015
DE Control vocabulary for diseases.
DS Uniprot
DR http://swissprot.isb-sib.ch/sdu/annotation/humdisease.txt, manually load to freud
DR gefiles.isb-sib.ch:/work/grp-sprot/sptr/current_release/humdisease.txt
UF monthly, linked to uniprot update
UR
CI
//
ID UniProtKB domain
AC CVDR-0010
DE Control vocabulary for domains, repeat and zinc fingers
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_domain.txt
UF monthly, linked to uniprot update
UR
CI
//
ID UniProtKB enzyme classification
AC CVDR-0014
DE Control vocabulary for enzyme classification and enzyme description.
DS Uniprot
DR gefiles.isb-sib.ch:/work/grp-sprot/sptr/current_release/enzyme.dat
DR gefiles.isb-sib.ch:/work/grp-sprot/sptr/current_release/enzclass.txt
UF monthly
UR http://www.expasy.org/enzyme/
CI
//
ID UniProtKB keywords
AC CVDR-0016
DE Control vocabulary for keywords
DS Uniprot
DR gefiles.isb-sib.ch:/work/grp-sprot/sptr/current_release/keywlist.txt
UF monthly, linked to uniprot update
UR
CI
//
ID UniProtKB metal
AC CVDR-0011
DE Control vocabulary for metal bound to protein.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_metal.txt
UF occasionally
UR
CI
//
ID UniProtKB organelle
AC CVDR-0013
DE Control vocabulary for organelles.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_organelles.txt
UF occasionally
UR
CI
//
ID UniProtKB pathways
AC CVDR-0017
DE Control vocabulary for metabolic pathways
DS Uniprot
DR http://www.grenoble.prabi.fr/obiwarehouse/download/unipathway/public/unipathway.obo
UF monthly, linked to uniprot update
UR
CI
//
ID UniProtKB posttranslational modifications
AC CVDR-0018
DE Control vocabulary for posttranslational modifications
DS Uniprot
DR gefiles.isb-sib.ch:/work/grp-sprot/sptr/current_release/ptmlist.txt
UF monthly, linked to uniprot update
UR
CI
//
ID UniProtKB region structure
AC CVDR-0012
DE Control vocabulary for protein region structure
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_region_structures.txt
UF occasionally
UR
CI
//
ID UniProtKB subcellular location
AC CVDR-0019
DE Control vocabulary for subcellular location, orientation and topology
DS Uniprot
DR gefiles.isb-sib.ch:/work/grp-sprot/sptr/current_release/subcell.txt
UF monthly, linked to uniprot update
UR
CI
//
ID UniProtKB topology
AC CVDR-0022
DE Control vocabulary for topology of regions for transmembrane proteins that span membrane compartments.
DS NextProt
DR freud.isb-sib.ch:/share/sib/common/Calipho/np/cv/cv_topological_domain.txt
UF occasionally
UR
CI
//
ID Human Adrenal Gland PeptideAtlas
AC CVDR-0100
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human Adrenal Gland samples.
DS PeptideAtlas human Adrenal Gland
DR ftp://pa10:paISB2xx%[email protected]/HumanAll/2018_peptide_list.zip
UF once or twice a year
UR http://www.peptideatlas.org
CI
//
ID Human Digestive System PeptideAtlas
AC CVDR-0101
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human Digestive System samples.
DS PeptideAtlas human Digestive System
DR ftp://pa10:paISB2xx%[email protected]/HumanAll/2018_peptide_list.zip
UF once or twice a year
UR http://www.peptideatlas.org
CI
//
ID Human Blood Cells PeptideAtlas
AC CVDR-0102
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human Blood Cells samples.
DS PeptideAtlas human Blood Cells
DR ftp://pa10:paISB2xx%[email protected]/HumanAll/2018_peptide_list.zip
UF once or twice a year
UR http://www.peptideatlas.org
CI
//
ID Human Blood Plasma PeptideAtlas
AC CVDR-0103
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human Blood Plasma samples.
DS PeptideAtlas human Blood Plasma
DR ftp://pa10:paISB2xx%[email protected]/HumanAll/2018_peptide_list.zip
UF once or twice a year
UR http://www.peptideatlas.org
CI
//
ID Human Brain PeptideAtlas
AC CVDR-0104
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human Brain samples.
DS PeptideAtlas human Brain
DR ftp://pa10:paISB2xx%[email protected]/HumanAll/2018_peptide_list.zip
UF once or twice a year
UR http://www.peptideatlas.org
CI
//
ID Human Breast PeptideAtlas
AC CVDR-0105
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human Breast samples.
DS PeptideAtlas human Breast
DR ftp://pa10:paISB2xx%[email protected]/HumanAll/2018_peptide_list.zip
UF once or twice a year
UR http://www.peptideatlas.org
CI
//
ID Human Cancer Cell Lines Digestive System PeptideAtlas
AC CVDR-0106
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human Cancer Cell Lines, Digestive System samples.
DS PeptideAtlas human Cancer Cell Lines Digestive System
DR ftp://pa10:paISB2xx%[email protected]/HumanAll/2018_peptide_list.zip
UF once or twice a year
UR http://www.peptideatlas.org
CI
//
ID Human Cancer Cell Lines Blood PeptideAtlas
AC CVDR-0107
DE Proteomics data (peptides): Integration of peptide sequences obtained by high-throughput mass spectrometry.
DE Human Cancer Cell Lines, Blood samples.