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103 changes: 103 additions & 0 deletions Changes.md
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## 2018-08-XX release

### Summary

* The upper level has been refactored to provide a more intuitive top down view
* Additional equivalence axioms to ONCOTREE
* Filter redundant mapping from SKOS relationships, fixes #282

### New classes

* [pulmonary branch stenosis](http://purl.obolibrary.org/obo/MONDO_0020420y)
* [myelofibrosis](http://purl.obolibrary.org/obo/MONDO_0044903)
* [metastatic squamous cell carcinoma](http://purl.obolibrary.org/obo/MONDO_0044907)
* [bladder urothelial papilloma](http://purl.obolibrary.org/obo/MONDO_0044906)
* [metastatic malignant neoplasm in the eye](http://purl.obolibrary.org/obo/MONDO_0044913)
* [extrarenal rhabdoid tumor](http://purl.obolibrary.org/obo/MONDO_0044916)
* [salivary duct carcinoma](http://purl.obolibrary.org/obo/MONDO_0044915)
* [metastatic malignant neoplasm in the spinal cord](http://purl.obolibrary.org/obo/MONDO_0044912)
* [T-lymphoblastic lymphoma](http://purl.obolibrary.org/obo/MONDO_0044917)
* [malignant renal pelvis neoplasm](http://purl.obolibrary.org/obo/MONDO_0044919)
* [paranasal sinus mucoepidermoid carcinoma](http://purl.obolibrary.org/obo/MONDO_0044956)
* [oral cavity carcinoma](http://purl.obolibrary.org/obo/MONDO_0044925)
* [acute myeloid leukemia with mutated CEBPA](http://purl.obolibrary.org/obo/MONDO_0044924)
* [oropharyngeal carcinoma](http://purl.obolibrary.org/obo/MONDO_0044926)
* [atypical lymphoproliferative disorder](http://purl.obolibrary.org/obo/MONDO_0044921)
* [acute myeloid leukemia with mutated NPM1](http://purl.obolibrary.org/obo/MONDO_0044923)
* [rectal carcinoma](http://purl.obolibrary.org/obo/MONDO_0044937)
* [benign lipomatous neoplasm](http://purl.obolibrary.org/obo/MONDO_0044983)
* [drug pseudoallergy](http://purl.obolibrary.org/obo/MONDO_0044982)
* [pseudoallergy](http://purl.obolibrary.org/obo/MONDO_0044981)
* [disease of signal transduction](http://purl.obolibrary.org/obo/MONDO_0044980)
* [disease of membrane bound organelle](http://purl.obolibrary.org/obo/MONDO_0044969)
* [abdominal and pelvic region disorder](http://purl.obolibrary.org/obo/MONDO_0044965)
* [oral cavity mucoepidermoid carcinoma](http://purl.obolibrary.org/obo/MONDO_0044964)
* [limb disorder](http://purl.obolibrary.org/obo/MONDO_0044967)
* [eosinophil disease](http://purl.obolibrary.org/obo/MONDO_0044972)
* [disease of macromolecular complex](http://purl.obolibrary.org/obo/MONDO_0044971)
* [disease of supramolecular complex](http://purl.obolibrary.org/obo/MONDO_0044974)
* [mitochondrial disease](http://purl.obolibrary.org/obo/MONDO_0044970)
* [disease by cell type](http://purl.obolibrary.org/obo/MONDO_0044979)
* [disease of catalytic activity](http://purl.obolibrary.org/obo/MONDO_0044976)
* [disease of transporter activity](http://purl.obolibrary.org/obo/MONDO_0044975)
* [disease of cell nucleus](http://purl.obolibrary.org/obo/MONDO_0044978)
* [disease of receptor activity](http://purl.obolibrary.org/obo/MONDO_0044977)
* [desmoplastic spitz nevus](http://purl.obolibrary.org/obo/MONDO_0044800)
* [early onset primary dystonia](http://purl.obolibrary.org/obo/MONDO_0044808)
* [inherited dystonia](http://purl.obolibrary.org/obo/MONDO_0044807)
* [acquired idiopathic torsion dystonia](http://purl.obolibrary.org/obo/MONDO_0044817)
* [familial idiopathic torsion dystonia](http://purl.obolibrary.org/obo/MONDO_0044816)
* [idiopathic torsion dystonia](http://purl.obolibrary.org/obo/MONDO_0044811)
* [childhood myelodysplastic syndrome](http://purl.obolibrary.org/obo/MONDO_0044873)
* [dysautonomia](http://purl.obolibrary.org/obo/MONDO_0044872)
* [coronary microvascular disease](http://purl.obolibrary.org/obo/MONDO_0044875)
* [refractory cytopenia of childhood](http://purl.obolibrary.org/obo/MONDO_0044874)
* [dystonia, focal, task-specific](http://purl.obolibrary.org/obo/MONDO_0044871)
* [acquired torsion dystonia](http://purl.obolibrary.org/obo/MONDO_0044870)
* [paraneoplastic cerebellar degeneration](http://purl.obolibrary.org/obo/MONDO_0044877)
* [drug hypersensitivity syndrome](http://purl.obolibrary.org/obo/MONDO_0044876)
* [pancreatic mucinous-cystic neoplasm](http://purl.obolibrary.org/obo/MONDO_0044879)
* [adult germ cell tumor](http://purl.obolibrary.org/obo/MONDO_0044878)
* [torsion dystonia](http://purl.obolibrary.org/obo/MONDO_0044843)
* [tonsillar lymphoma](http://purl.obolibrary.org/obo/MONDO_0044884)
* [tonsillar lipoma](http://purl.obolibrary.org/obo/MONDO_0044885)
* [cystic tumor of the pancreas](http://purl.obolibrary.org/obo/MONDO_0044880)
* [hematopoietic and lymphoid cell neoplasm](http://purl.obolibrary.org/obo/MONDO_0044881)
* [central nervous system non-hodgkin lymphoma](http://purl.obolibrary.org/obo/MONDO_0044887)
* [high grade B-cell lymphoma](http://purl.obolibrary.org/obo/MONDO_0044889)
* [X-linked congenital stationary night blindness](http://purl.obolibrary.org/obo/MONDO_0044749)
* [anaplasmosis in cattle](http://purl.obolibrary.org/obo/MONDO_0044748)
* [human anaplasmosis](http://purl.obolibrary.org/obo/MONDO_0044747)
* [zoonotic bacterial infection](http://purl.obolibrary.org/obo/MONDO_0044746)
* [chronic diarrheal disease](http://purl.obolibrary.org/obo/MONDO_0044751)
* [lumbar spinal stenosis](http://purl.obolibrary.org/obo/MONDO_0044753)
* [lassa virus infectious disease](http://purl.obolibrary.org/obo/MONDO_0044750)
* [desmoplastic melanoma](http://purl.obolibrary.org/obo/MONDO_0044785)
* [myxoma](http://purl.obolibrary.org/obo/MONDO_0044784)
* [nasal cavity and paranasal sinus squamous cell carcinoma](http://purl.obolibrary.org/obo/MONDO_0044787)
* [solid pseudopapillary neoplasm of the pancreas](http://purl.obolibrary.org/obo/MONDO_0044786)
* [nephrotic syndrome of childhood - steroid sensitive](http://purl.obolibrary.org/obo/MONDO_0044781)
* [solid papillary breast carcinoma](http://purl.obolibrary.org/obo/MONDO_0044783)
* [esophageal ulcer](http://purl.obolibrary.org/obo/MONDO_0044782)
* [digital papillary eccrine carcinoma](http://purl.obolibrary.org/obo/MONDO_0044789)
* [perihilar intrahepatic cholangiocarcinoma](http://purl.obolibrary.org/obo/MONDO_0044788)
* [obsolete congenital melanocytic nevus](http://purl.obolibrary.org/obo/MONDO_0044790)
* [spindle cell nevus](http://purl.obolibrary.org/obo/MONDO_0044796)
* [epithelioid cell nevus](http://purl.obolibrary.org/obo/MONDO_0044795)
* [desmoplastic nevus](http://purl.obolibrary.org/obo/MONDO_0044797)
* [large congenital melanocytic nevus](http://purl.obolibrary.org/obo/MONDO_0044792)
* [combined hepatocellular carcinoma and cholangiocarcinoma](http://purl.obolibrary.org/obo/MONDO_0044791)
* [benign melanocytic skin nevus](http://purl.obolibrary.org/obo/MONDO_0044794)
* [spitz nevus](http://purl.obolibrary.org/obo/MONDO_0044793)
* [diarrheal disease secondary to decreased bowel motility](http://purl.obolibrary.org/obo/MONDO_0044763)
* [diarrheal disease secondary to increased bowel motility](http://purl.obolibrary.org/obo/MONDO_0044762)
* [steroid-resistant nephrotic syndrome](http://purl.obolibrary.org/obo/MONDO_0044765)
* [benign choroid plexus neoplasm](http://purl.obolibrary.org/obo/MONDO_0044764)
* [childhood adrenal gland pheochromocytoma](http://purl.obolibrary.org/obo/MONDO_0044767)
* [obsolete Marfan Syndrome 3](http://purl.obolibrary.org/obo/MONDO_0044766)
* [vagus nerve paraganglioma](http://purl.obolibrary.org/obo/MONDO_0044768)
* [premature ovarian failure 10](http://purl.obolibrary.org/obo/MONDO_0044776)
* [nodular lymphocyte predominant Hodgkin lymphoma](http://purl.obolibrary.org/obo/MONDO_0044778)
* [premature ovarian failure 14](http://purl.obolibrary.org/obo/MONDO_0044777)


## 2018-08-03 Release

This release includes more complete mappings to UMLS/MEDGEN
Expand Down
93 changes: 37 additions & 56 deletions src/ontology/Makefile
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Expand Up @@ -54,7 +54,7 @@ all: test all_artefacts
# ----------------------------------------
# Artefacts
# ----------------------------------------
ONTOLOGY_IMPORTS = uberon cl go pato ro hp mf ncbitaxon chebi envo foodon
ONTOLOGY_IMPORTS = uberon cl go pato ro hp mf ncbitaxon chebi envo ecto hgnc foodon
IMPORT_ROOTS = $(patsubst %, imports/%_import, $(ONTOLOGY_IMPORTS)) imports/equivalencies
IMPORT_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl $(n).obo $(n).json) imports/axioms.owl
IMPORT_FILES_OWL = $(foreach n,$(IMPORT_ROOTS), $(n).owl) imports/axioms.owl
Expand Down Expand Up @@ -113,7 +113,7 @@ osf_upload_direct:
ANN = annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$@.owl

filtered.obo: $(SRC)
perl -ne 'print unless (m@^xref: (Orphanet|OMIM|DOID|EFO|NCIT|SCTID|MESH|UMLS):@ && !(m@equivalentTo@))' $< | grep -v '^property_value: confidence' | grep -v '^property_value: excluded_subClassOf' | grep -v 'relationship: disease_has_basis_in_dysfunction_of HGNC:' > $@.tmp && mv $@.tmp $@
perl -ne 'print unless (m@^xref: (Orphanet|OMIM|DOID|EFO|NCIT|SCTID|MESH|UMLS):@ && !(m@equivalent@i))' $< | grep -v '^property_value: confidence' | grep -v '^property_value: excluded_subClassOf' | egrep -v 'relationship: disease_has_basis_in_dysfunction_of (hgnc|HGNC|NCBIGene):' > $@.tmp && mv $@.tmp $@
#egrep -v 'MONDO:(subClassOf|superClassOf|relatedTo)' $< > $@

skos.ttl: $(SRC)
Expand Down Expand Up @@ -255,10 +255,11 @@ imports/%_import.owl: mirror/%.owl imports/%_terms.txt

# we use owltools for making the obo file until: https://github.com/ontodev/robot/issues/64
imports/%_import.obo: imports/%_import.owl
$(OWLTOOLS) $(USECAT) $< -o -f obo --no-check $@.tmp && mv $@.tmp $@
$(OWLTOOLS) $(USECAT) $< -o -f obo --no-check $@.tmp && grep -v ^owl-axioms $@.tmp > $@


imports/%_terms.txt: $(SRC)
edit-merged.owl: $(SRC)
robot merge -c true -i $< -o $@
imports/%_terms.txt: edit-merged.owl
robot query -f tsv -i $< -s ../sparql/classes.sparql $@.tmp && grep -hi $* $@.tmp imports/$*_terms.txt | perl -npe 's@^\<@@;s@>$$@@' | sort -u > $@

# ----------------------------------------
Expand Down Expand Up @@ -300,11 +301,10 @@ NEWAXTEST: mondo-edit.owl new.owl

# these live in the ../sparql directory, and have suffix -violation.sparql
# adding the name here will make the violation check live
EDIT_CHECKS = subclass-cycle equivalent-classes trailing-whitespace owldef-self-reference xref-syntax nolabels undeclared-synonym-type undeclared-subset same-label

MAIN_OWL_CHECKS = subclass-cycle equivalent-classes trailing-whitespace owldef-self-reference xref-syntax nolabels undeclared-synonym-type undeclared-subset same-label

MAIN_OBO_CHECKS = subclass-cycle equivalent-classes trailing-whitespace owldef-self-reference xref-syntax nolabels undeclared-synonym-type undeclared-subset same-label
CORE_CHECKS = subclass-cycle equivalent-classes trailing-whitespace owldef-self-reference xref-syntax nolabels undeclared-synonym-type undeclared-subset same-label
EDIT_CHECKS = $(CORE_CHECKS)
MAIN_OWL_CHECKS = $(CORE_CHECKS) no-superclass
MAIN_OBO_CHECKS = $(CORE_CHECKS) no-superclass

QSRC = $(SRC)-noimports.owl

Expand Down Expand Up @@ -531,59 +531,23 @@ mirror/ncit-disease.obo: mirror/ncit-disease.owl
mirror/rdo.obo:
wget --no-check-certificate ftp://ftp.rgd.mcw.edu/pub/ontology/disease/RDO.obo -O $@ && touch $@

mirror/ordo_orphanet.owl.zip:
wget --no-check-certificate -nd -P mirror http://www.orphadata.org/data/ORDO/ordo_orphanet.owl.zip && touch $@

mirror/ordo_orphanet.owl: mirror/ordo_orphanet.owl.zip
unzip mirror/ordo_orphanet.owl.zip -d mirror
touch $@

mirror/medgen-disease-extract.owl: mirror/medgen-disease-extract.obo
owltools $< -o $@.tmp && perl -npe $(FIX_URI_EXPR) $@.tmp > $@

mirror/dipper-%.ttl:
wget --no-check-certificate https://data.monarchinitiative.org/ttl/$*.ttl -O $@

wget --no-check-certificate https://data.monarchinitiative.org/ttl/$*.ttl -O $@.tmp && perl -npe 's@http://www.genenames.org/cgi-bin/gene_symbol_report\\?hgnc_id=@http://identifiers.org/hgnc/@g' $@.tmp > $@

mirror/dipper-%.obo: mirror/dipper-%.ttl
robot convert -i $< -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@

# ~~~~~~~~
# ORDO
# ~~~~~~~~
mirror/hgnc.owl: mirror/dipper-hgnc.ttl
robot query --format ttl -c ../sparql/construct-hgnc.sparql $@ -i $<
# robot query construct
# owltools $< --remove-axioms -t EquivalentClasses -o $@
# owltools $< --remove-dangling -o $@
# owltools $< --merge-equivalence-sets -s http://identifiers.org/hgnc/ 20 -o $@


# STEP 1: DOWNLOAD
mirror/obo_orphanet_1.owl: mirror/ordo_orphanet.owl
owltools $< $(EFO2OBO_OPTS) -o $@.tmp && mv $@.tmp $@

# STEP 2: Fix XREFs
mirror/obo_orphanet_2.owl: mirror/obo_orphanet_1.owl
perl -npe 's@MeSH:@MESH:@;s@ICD-10:@ICD10:@;' $< > $@.tmp && mv $@.tmp $@

# STEP 2b: Create is-a from part-of
mirror/obo_orphanet_sc.owl: mirror/obo_orphanet_2.owl
robot query --format ttl -c ../sparql/construct-subclass-from-part-of.sparql $@ -i $<

# STEP 2c: Create subsets based on subClass to sub-root level
mirror/obo_orphanet_subsets.owl: mirror/obo_orphanet_2.owl
robot query --format ttl -c ../sparql/construct-ordo-subsets.sparql $@ -i $<

# STEP 3: merge 2b and 2c in to 2
mirror/obo_orphanet_3.owl: mirror/obo_orphanet_2.owl mirror/obo_orphanet_sc.owl mirror/obo_orphanet_subsets.owl
owltools $^ --merge-support-ontologies -o $@

# STEP 3b: make an .obo file
mirror/obo_orphanet_3.obo: mirror/obo_orphanet_3.owl
owltools $< -o -f obo $@.tmp && grep -v ^owl-axioms $@.tmp > $@

# STEP 4: Remove part-ofs (see 2b, we have these as subClassOf now)
mirror/obo_orphanet_4.obo: mirror/obo_orphanet_3.obo
grep -v '^relationship: BFO:0000050' $< > $@

mirror/obo_orphanet.obo: mirror/obo_orphanet_4.obo
cp $< $@
mirror/obo_orphanet.owl: mirror/obo_orphanet.obo
owltools $< -o $@.tmp && perl -npe 's@http://purl.obolibrary.org/obo/Orphanet_@http://www.orpha.net/ORDO/Orphanet_@g' $@.tmp > $@

mirror/omia.ttl:
wget --no-check-certificate http://data.monarchinitiative.org/ttl/omia.ttl -O $@ && touch $@
.PRECIOUS: mirror/omia.ttl
Expand Down Expand Up @@ -751,7 +715,24 @@ omim2medgen.obo: mim2gene_medgen
# remember to clear tmp/ dir for fresh start
# mondo_queries requires for prefixes
all_unique.tsv:
rdfmatch -p MONDO -l -c ../plq/mondo_queries.pro -X tmp -A void.ttl -f tsv -v -i all unique_match > $@
rdfmatch -p MONDO -l -c ../plq/mondo_queries.pro -X tmp -A void.ttl -f tsv -v -i all -i skos.ttl unique_match > $@

all_unique_fresh: clean_tmp all_unique.tsv
clean_tmp:
rm tmp/*

# ----------------------------------------
# Metaclasses
# ----------------------------------------
disorder-by-%.tsv: mondo-edit.obo
blip-findall -r uberonp -r cell -r go -i $< "class_cdef(C,cdef('MONDO:0000001',[disease_has_location=A])),subclassRT(A,'$(subst _,:,$*)')" -select C-A -no_pred -use_tabs -label > $@.tmp && sort -u $@.tmp > $@

disorder-by-anatomical-region.tsv: disorder-by-UBERON_0000475.tsv
cp $< $@
disorder-by-anatomical-system.tsv: disorder-by-UBERON_0000467.tsv
cp $< $@
disorder-by-cell.tsv: disorder-by-CL_0000000.tsv
cp $< $@

# ----------------------------------------
# Anns
Expand Down
2 changes: 2 additions & 0 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -15,6 +15,8 @@
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/mondo/imports/envo_import.owl" uri="imports/envo_import.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/mondo/imports/ecto_import.owl" uri="imports/ecto_import.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/mondo/imports/foodon_import.owl" uri="imports/foodon_import.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/mondo/imports/nbo_import.owl" uri="imports/nbo_import.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/mondo/imports/hgnc_import.owl" uri="imports/hgnc_import.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/mondo/imports/axioms.owl" uri="imports/axioms.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/mondo/imports/equivalencies.owl" uri="imports/equivalencies.owl"/>
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base=""/>
Expand Down
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