Skip to content

Commit

Permalink
Merge branch 'cjm'
Browse files Browse the repository at this point in the history
  • Loading branch information
@cmungall
cmungall committed May 30, 2018
2 parents aa15d92 + d8e207e commit 78f401d
Show file tree
Hide file tree
Showing 24 changed files with 5,461 additions and 2,630 deletions.
98 changes: 98 additions & 0 deletions Changes.md
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,101 @@
## 2018-05-29 Release

New classes:

* [vascular bone neoplasm](http://purl.obolibrary.org/obo/MONDO_0024499)
* [glioma susceptibility 1](http://purl.obolibrary.org/obo/MONDO_0024498)
* [familial chronic mucocutaneous candidiasis](http://purl.obolibrary.org/obo/MONDO_0024486)
* [papillary urothelial hyperplasia](http://purl.obolibrary.org/obo/MONDO_0024485)
* [tumor grading characteristic](http://purl.obolibrary.org/obo/MONDO_0024488)
* [nail infection](http://purl.obolibrary.org/obo/MONDO_0024487)
* [general tumor grading characteristic](http://purl.obolibrary.org/obo/MONDO_0024489)
* [dermatosis of eyelid](http://purl.obolibrary.org/obo/MONDO_0024480)
* [eccrine sweat gland hamartoma](http://purl.obolibrary.org/obo/MONDO_0024482)
* [skin appendage disease](http://purl.obolibrary.org/obo/MONDO_0024481)
* [urothelial hyperplasia](http://purl.obolibrary.org/obo/MONDO_0024483)
* [spondyloarthropathy, susceptibility to](http://purl.obolibrary.org/obo/MONDO_0024512)
* [familial acne inversa](http://purl.obolibrary.org/obo/MONDO_0024516)
* [reactive thrombocytosis](http://purl.obolibrary.org/obo/MONDO_0024518)
* [schwannomatosis 1](http://purl.obolibrary.org/obo/MONDO_0024517)
* [renal hypodysplasia/aplasia 1](http://purl.obolibrary.org/obo/MONDO_0024519)
* [appendix neuroendocrine neoplasm](http://purl.obolibrary.org/obo/MONDO_0024501)
* [duodenal neuroendocrine neoplasm](http://purl.obolibrary.org/obo/MONDO_0024500)
* [digestive system neuroendocrine neoplasm](http://purl.obolibrary.org/obo/MONDO_0024503)
* [gallbladder neuroendocrine neoplasm](http://purl.obolibrary.org/obo/MONDO_0024502)
* [disorder of anatomical region](http://purl.obolibrary.org/obo/MONDO_0024505)
* [enterochromaffin cell serotonin-producing pancreatic neuroendocrine tumor](http://purl.obolibrary.org/obo/MONDO_0024504)
* [aniridia 1](http://purl.obolibrary.org/obo/MONDO_0024507)
* [Adams-Oliver syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024506)
* [epilepsy, hot water, 1](http://purl.obolibrary.org/obo/MONDO_0024508)
* [bethlem myopathy 1](http://purl.obolibrary.org/obo/MONDO_0024530)
* [otofaciocervical syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024532)
* [myopathy, tubular aggregate, 1](http://purl.obolibrary.org/obo/MONDO_0024531)
* [Dowling-Degos disease 1](http://purl.obolibrary.org/obo/MONDO_0024534)
* [pulmonary hypertension, primary, 1](http://purl.obolibrary.org/obo/MONDO_0024533)
* [glucocorticoid deficiency 1](http://purl.obolibrary.org/obo/MONDO_0024536)
* [Singleton-Merten syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024535)
* [basal ganglia calcification, idiopathic, 1](http://purl.obolibrary.org/obo/MONDO_0024538)
* [Brown-Vialetto-van Laere syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024537)
* [choroidal dystrophy, central areolar, 1](http://purl.obolibrary.org/obo/MONDO_0024539)
* [AAA1](http://purl.obolibrary.org/obo/MONDO_0024521)
* [renal hypodysplasia/aplasia 3](http://purl.obolibrary.org/obo/MONDO_0024520)
* [aortic valve disease 1](http://purl.obolibrary.org/obo/MONDO_0024523)
* [amyloidosis, primary localized cutaneous, 1](http://purl.obolibrary.org/obo/MONDO_0024522)
* [FRTS1](http://purl.obolibrary.org/obo/MONDO_0024525)
* [DUH1](http://purl.obolibrary.org/obo/MONDO_0024524)
* [GFND1](http://purl.obolibrary.org/obo/MONDO_0024527)
* [Zimmermann-Laband syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024526)
* [MVP1](http://purl.obolibrary.org/obo/MONDO_0024529)
* [progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant 1](http://purl.obolibrary.org/obo/MONDO_0024528)
* [linear skin defects with multiple congenital anomalies 1](http://purl.obolibrary.org/obo/MONDO_0024552)
* [lymphoproliferative syndrome, X-linked, 1](http://purl.obolibrary.org/obo/MONDO_0024551)
* [D-2-hydroxyglutaric aciduria 1](http://purl.obolibrary.org/obo/MONDO_0024554)
* [myopathy, lactic acidosis, and sideroblastic anemia 1](http://purl.obolibrary.org/obo/MONDO_0024553)
* [epilepsy, familial focal, with variable foci 1](http://purl.obolibrary.org/obo/MONDO_0024556)
* [megalencephalic leukoencephalopathy with subcortical cysts 1](http://purl.obolibrary.org/obo/MONDO_0024555)
* [radioulnar synostosis with amegakaryocytic thrombocytopenia 1](http://purl.obolibrary.org/obo/MONDO_0024558)
* [ataxia-telangiectasia-like disorder 1](http://purl.obolibrary.org/obo/MONDO_0024557)
* [frontometaphyseal dysplasia 1](http://purl.obolibrary.org/obo/MONDO_0024550)
* [AAT1](http://purl.obolibrary.org/obo/MONDO_0024559)
* [trichohepatoenteric syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024541)
* [Jervell and Lange-Nielsen syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024540)
* [brittle cornea syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024543)
* [cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024542)
* [Miyoshi muscular dystrophy 1](http://purl.obolibrary.org/obo/MONDO_0024545)
* [Heimler syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024544)
* [pancreatic agenesis 1](http://purl.obolibrary.org/obo/MONDO_0024547)
* [hypertrophic osteoarthropathy, primary, autosomal recessive, 1](http://purl.obolibrary.org/obo/MONDO_0024546)
* [MCOPCB1](http://purl.obolibrary.org/obo/MONDO_0024549)
* [peeling skin syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024548)
* [hyperparathyroidism 4](http://purl.obolibrary.org/obo/MONDO_0024570)
* [herpes simplex encephalitis, susceptibility to, 1](http://purl.obolibrary.org/obo/MONDO_0024563)
* [sick sinus syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024562)
* [ectodermal dysplasia-syndactyly syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024565)
* [cerebroretinal microangiopathy with calcifications and cysts 1](http://purl.obolibrary.org/obo/MONDO_0024564)
* [hypotonia, infantile, with psychomotor retardation and characteristic facies 1](http://purl.obolibrary.org/obo/MONDO_0024567)
* [febrile seizures, familial, 11](http://purl.obolibrary.org/obo/MONDO_0024566)
* [OPA8](http://purl.obolibrary.org/obo/MONDO_0024569)
* [infantile liver failure syndrome 1](http://purl.obolibrary.org/obo/MONDO_0024568)
* [macular dystrophy, vitelliform, 3](http://purl.obolibrary.org/obo/MONDO_0024561)
* [PDA1](http://purl.obolibrary.org/obo/MONDO_0024560)
* [squamous cell intraepithelial neoplasia](http://purl.obolibrary.org/obo/MONDO_0024475)
* [intraepithelial neoplasia](http://purl.obolibrary.org/obo/MONDO_0024474)
* [liver and intrahepatic bile duct neoplasm](http://purl.obolibrary.org/obo/MONDO_0024477)
* [epithelial neoplasm of rectum](http://purl.obolibrary.org/obo/MONDO_0024476)
* [epithelial tumor of colon](http://purl.obolibrary.org/obo/MONDO_0024479)
* [mesenchymal hamartoma](http://purl.obolibrary.org/obo/MONDO_0024478)
* [Astrakhan spotted fever](http://purl.obolibrary.org/obo/MONDO_0024473)
* [Boutonneuse fever](http://purl.obolibrary.org/obo/MONDO_0024472)
* [tumor grade 3 or 4, general grading system](http://purl.obolibrary.org/obo/MONDO_0024497)
* [tumor grade 2 or 3, general grading system](http://purl.obolibrary.org/obo/MONDO_0024496)
* [tumor grade 1, general grading system](http://purl.obolibrary.org/obo/MONDO_0024491)
* [tumor grade X, general grading system](http://purl.obolibrary.org/obo/MONDO_0024490)
* [tumor grade 3, general grading system](http://purl.obolibrary.org/obo/MONDO_0024493)
* [tumor grade 2, general grading system](http://purl.obolibrary.org/obo/MONDO_0024492)
* [tumor grade 1 or 2, general grading system](http://purl.obolibrary.org/obo/MONDO_0024495)
* [tumor grade 4, general grading system](http://purl.obolibrary.org/obo/MONDO_0024494)


## 2018-05-20 Release

New classes:
Expand Down
16 changes: 13 additions & 3 deletions src/ontology/Makefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -386,6 +386,10 @@ imports/equivalencies.owl: ../sparql/construct-ecs-from-xrefs.sparql $(SRC)
imports/equivalencies.obo: imports/equivalencies.owl
robot convert -i $< -o $@

clean_imports: $(patsubst %, clean-mirror-%, $(ONTOLOGY_IMPORTS))
clean-mirror-%:
test -f mirror/%.owl && rm mirror/%.owl || echo 'no mirror file'

#imports/equivalencies.owl: $(SRC)
# ../utils/xrefs2axioms.pl $< > [email protected] && owltools [email protected] -o $@

Expand Down Expand Up @@ -421,7 +425,7 @@ trigger-mirror:
touch $@

# clone remote ontology locally, perfoming some excision of relations and annotations
mirror/%.owl: trigger-mirror
mirror/%.owl:
$(OWLTOOLS) $(OBO)/$*.owl --remove-annotation-assertions -l -s -d -r --remove-dangling-annotations --remove-axiom-annotations -o $@
.PRECIOUS: mirror/%.owl

Expand All @@ -430,7 +434,7 @@ mirror/ncbitaxon.owl:
.PRECIOUS: mirror/ncbitaxon.owl

# hp.owl currently contains many stray root classes
mirror/hp.obo: trigger-mirror
mirror/hp.obo:
wget --no-check-certificate $(OBO)/hp.obo -O $@.tmp && mv $@.tmp $@ && touch $@
.PRECIOUS: mirror/hp.obo
mirror/hp.owl: mirror/hp.obo
Expand Down Expand Up @@ -615,7 +619,10 @@ testcombo-%: mondo-edit.obo disjoint_sibs.owl imports/equivalencies.owl mirror/%
owltools --use-catalog $^ --merge-support-ontologies --run-reasoner -r elk -u -m compare/bad-$*.owl

debug.owl: mondo-edit.obo disjoint_sibs.owl imports/equivalencies.owl
owltools --use-catalog $^ --merge-support-ontologies --run-reasoner -r elk -u -m $@
owltools --use-catalog $^ --merge-support-ontologies --run-reasoner -r elk -u -m $@ | grep -v ^INFERENCE

debug2.owl: mondo.owl disjoint_sibs.owl imports/equivalencies.owl
owltools --use-catalog $^ --merge-support-ontologies --run-reasoner -r elk -u -m $@ | grep -v ^INFERENCE

# ----------------------------------------
# Lexical mapping
Expand Down Expand Up @@ -704,6 +711,9 @@ d2symp-wd.tsv:
weights.tsv:
pl2sparql -f tsv -e -i mondo-edit.owl -c ../plq/kboom_weights.pro w > $@

weights-mg.tsv:
pl2sparql -f tsv -e -i mondo-edit.owl -i mirror/medgen-disease-extract.owl -c ../plq/kboom_weights.pro w > $@

ptable.tsv: weights.tsv
../utils/softmax-weights.py $< > $@

Expand Down
1 change: 1 addition & 0 deletions src/ontology/imports/cl_terms.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ http://purl.obolibrary.org/obo/CL_0000057
http://purl.obolibrary.org/obo/CL_0000059
http://purl.obolibrary.org/obo/CL_0000066
http://purl.obolibrary.org/obo/CL_0000071
http://purl.obolibrary.org/obo/CL_0000076
http://purl.obolibrary.org/obo/CL_0000084
http://purl.obolibrary.org/obo/CL_0000097
http://purl.obolibrary.org/obo/CL_0000100
Expand Down
94 changes: 94 additions & 0 deletions src/ontology/imports/go_import.obo
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2141,6 +2141,18 @@ name: collagen type XI trimer
def: "A collagen heterotrimer containing type XI alpha chains in alpha1(XI)alpha2(XI)alpha3(XI) trimers; type XI collagen triple helices associate to form fibrils." []
is_a: GO:0005583 ! fibrillar collagen trimer

[Term]
id: GO:0005593
name: FACIT collagen trimer
def: "A collagen trimer that associates with collagen fibrils and consists of collagen monomers that contain two or more relatively short triple-helical domains connected by non-triple-helical sequences." []
is_a: GO:0005581 ! collagen trimer

[Term]
id: GO:0005594
name: collagen type IX trimer
def: "A collagen heterotrimer containing type IX alpha chains in alpha1(IX)alpha2(IX)alpha3(IX) trimers; type IX collagen triple helices associate to form a structure that links glycosaminoglycans to type II collagen fibrils." []
is_a: GO:0005593 ! FACIT collagen trimer

[Term]
id: GO:0005604
name: basement membrane
Expand Down Expand Up @@ -5885,6 +5897,24 @@ def: "The directed movement of an organic hydroxy compound (organic alcohol) int
synonym: "organic alcohol transport" EXACT []
is_a: GO:0071702 ! organic substance transport

[Term]
id: GO:0015888
name: thiamine transport
def: "The directed movement of thiamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Thiamine is vitamin B1, a water soluble vitamin present in fresh vegetables and meats, especially liver." []
synonym: "thiamin transport" EXACT []
synonym: "vitamin B1 transport" EXACT []
is_a: GO:0015893 ! drug transport
is_a: GO:0045117 ! azole transport
is_a: GO:0051180 ! vitamin transport
is_a: GO:0072348 ! sulfur compound transport

[Term]
id: GO:0015893
name: drug transport
def: "The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." []
is_a: GO:0006810 ! transport
relationship: BFO:0000050 GO:0042493 ! part of response to drug

[Term]
id: GO:0015925
name: galactosidase activity
Expand Down Expand Up @@ -9827,6 +9857,14 @@ synonym: "hormone synthesis" EXACT []
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0042445 ! hormone metabolic process

[Term]
id: GO:0042493
name: response to drug
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease." []
synonym: "drug resistance" RELATED []
synonym: "drug susceptibility/resistance" RELATED []
is_a: GO:0042221 ! response to chemical

[Term]
id: GO:0042552
name: myelination
Expand Down Expand Up @@ -11030,6 +11068,13 @@ is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0044249 ! cellular biosynthetic process
is_a: GO:0046486 ! glycerolipid metabolic process

[Term]
id: GO:0045117
name: azole transport
def: "The directed movement of azoles, heterocyclic compounds found in many biologically important substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." []
is_a: GO:0071702 ! organic substance transport
is_a: GO:0071705 ! nitrogen compound transport

[Term]
id: GO:0045121
name: membrane raft
Expand Down Expand Up @@ -13855,6 +13900,13 @@ synonym: "single organism localization" RELATED []
synonym: "single-organism localization" RELATED []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0051180
name: vitamin transport
def: "The directed movement of vitamins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." []
synonym: "vitamin or cofactor transport" BROAD []
is_a: GO:0006810 ! transport

[Term]
id: GO:0051186
name: cofactor metabolic process
Expand Down Expand Up @@ -15759,6 +15811,13 @@ synonym: "monocarboxylic acid synthesis" EXACT []
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0046394 ! carboxylic acid biosynthetic process

[Term]
id: GO:0072348
name: sulfur compound transport
def: "The directed movement of compounds that contain sulfur, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." []
synonym: "sulfur-containing compound transport" EXACT []
is_a: GO:0006810 ! transport

[Term]
id: GO:0072350
name: tricarboxylic acid metabolic process
Expand Down Expand Up @@ -21400,6 +21459,41 @@ intersection_of: GO:0008150 ! biological_process
intersection_of: RO:0002213 GO:0006974 ! positively regulates cellular response to DNA damage stimulus
relationship: RO:0002213 GO:0006974 ! positively regulates cellular response to DNA damage stimulus

[Term]
id: GO:2001023
name: regulation of response to drug
def: "Any process that modulates the frequency, rate or extent of response to drug." []
synonym: "regulation of drug resistance" RELATED []
synonym: "regulation of drug susceptibility/resistance" RELATED []
is_a: GO:0048583 ! regulation of response to stimulus
intersection_of: GO:0008150 ! biological_process
intersection_of: RO:0002211 GO:0042493 ! regulates response to drug
relationship: RO:0002211 GO:0042493 ! regulates response to drug

[Term]
id: GO:2001024
name: negative regulation of response to drug
def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to drug." []
synonym: "negative regulation of drug resistance" RELATED []
synonym: "negative regulation of drug susceptibility/resistance" RELATED []
is_a: GO:0048585 ! negative regulation of response to stimulus
is_a: GO:2001023 ! regulation of response to drug
intersection_of: GO:0008150 ! biological_process
intersection_of: RO:0002212 GO:0042493 ! negatively regulates response to drug
relationship: RO:0002212 GO:0042493 ! negatively regulates response to drug

[Term]
id: GO:2001025
name: positive regulation of response to drug
def: "Any process that activates or increases the frequency, rate or extent of response to drug." []
synonym: "positive regulation of drug resistance" RELATED []
synonym: "positive regulation of drug susceptibility/resistance" RELATED []
is_a: GO:0048584 ! positive regulation of response to stimulus
is_a: GO:2001023 ! regulation of response to drug
intersection_of: GO:0008150 ! biological_process
intersection_of: RO:0002213 GO:0042493 ! positively regulates response to drug
relationship: RO:0002213 GO:0042493 ! positively regulates response to drug

[Term]
id: GO:2001141
name: regulation of RNA biosynthetic process
Expand Down
Loading

0 comments on commit 78f401d

Please sign in to comment.