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1 parent 5e0c0fe commit 82e71b97cdc4c93259494ae69d354fd6640cc702 @cmungall cmungall committed Dec 5, 2011
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@@ -695,7 +695,6 @@ fly_gene_phen_uber.txt:
human_gene_phen_anat.txt:
blip-findall -debug index -r omim2gene -r fma -r human_phenotype_xp -index "metadata_db:entity_xref(1,1)" -r gene/9606 -i phenotype_annotation.txt -i adhoc_uberon.pro human_ensgene_anat/4 > $@.tmp && sort -u $@.tmp > $@
-
HMD_HGNC_Accession.rpt:
wget ftp://ftp.informatics.jax.org/pub/reports/HMD_HGNC_Accession.rpt
@@ -868,7 +867,7 @@ template-%.txt:
# TAXON MODULES
# ----------------------------------------
# amniote = 32524
-all_taxmods: uberon-taxmod-amniote.owl uberon-taxmod-aves.owl
+all_taxmods: uberon-taxmod-amniote.owl uberon-taxmod-aves.owl uberon-taxmod-euarchontoglires.owl
#uberon-taxmod-amniote.ids: uberon.obo
# blip-findall -table_pred ontol_db:subclassRT/2 -r taxslim -i uberon_edit.obo -i $< -consult adhoc_uberon.pro "class_in_taxon_slim(X,'NCBITaxon:32524')" -select X > $@
@@ -878,12 +877,15 @@ all_taxmods: uberon-taxmod-amniote.owl uberon-taxmod-aves.owl
TAXFILTER = owltools uberon.obo uberon_edit.obo ncbi_taxon_slim.obo --merge-support-ontologies --make-taxon-set -s UBERON
uberon-taxmod-tetrapod.ids: merged_closure-ontol_db.pro
- blip-findall -table_pred ontol_db:subclassRT/2 -r taxslim -i uberon_edit.obo -i $< -consult adhoc_uberon.pro "class_in_taxon_slim(X,'NCBITaxon:32523')" -select X > $@
+ $(TAXFILTER) NCBITaxon:32523 > $@.tmp && grep ^UBERON $@.tmp > $@
+# blip-findall -table_pred ontol_db:subclassRT/2 -r taxslim -i uberon_edit.obo -i $< -consult adhoc_uberon.pro "class_in_taxon_slim(X,'NCBITaxon:32523')" -select X > $@.tmp && mv $@.tmp $@
uberon-taxmod-amniote.ids: uberon.obo
$(TAXFILTER) NCBITaxon:32524 > $@.tmp && grep ^UBERON $@.tmp > $@
# blip-findall -table_pred ontol_db:subclassRT/2 -r taxslim -i uberon_edit.obo -i $< -consult adhoc_uberon.pro "class_in_taxon_slim(X,'NCBITaxon:32524')" -select X > $@
uberon-taxmod-mammal.ids: merged_closure-ontol_db.pro
- blip-findall -table_pred ontol_db:subclassRT/2 -r taxslim -i uberon_edit.obo -i $< -consult adhoc_uberon.pro "class_in_taxon_slim(X,'NCBITaxon:40674')" -select X > $@
+ $(TAXFILTER) NCBITaxon:40674 > $@.tmp && grep ^UBERON $@.tmp > $@
+uberon-taxmod-euarchontoglires.ids: merged_closure-ontol_db.pro
+ $(TAXFILTER) NCBITaxon:314146 > $@.tmp && grep ^UBERON $@.tmp > $@
uberon-taxmod-sauropsid.ids: merged_closure-ontol_db.pro
blip-findall -table_pred ontol_db:subclassRT/2 -r taxslim -i uberon_edit.obo -i $< -consult adhoc_uberon.pro "class_in_taxon_slim(X,'NCBITaxon:8457')" -select X > $@
uberon-taxmod-aves.ids: uberon.obo
@@ -923,6 +925,8 @@ release: mod/bridges all_taxmods
cp uberon-taxmod-amniote.owl $(RELDIR)/subsets/amniote-basic.owl ;\
cp uberon-taxmod-aves.obo $(RELDIR)/subsets/aves-basic.obo ;\
cp uberon-taxmod-aves.owl $(RELDIR)/subsets/aves-basic.owl ;\
+ cp uberon-taxmod-euarchontoglires.obo $(RELDIR)/subsets/euarchontoglires-basic.obo ;\
+ cp uberon-taxmod-euarchontoglires.owl $(RELDIR)/subsets/euarchontoglires-basic.owl ;\
cp mod/*.{obo,owl} $(RELDIR)/bridge/ ;\
cp composite-{vertebrate,metazoan}.{obo,owl} $(RELDIR) ;\
cp uberon-simple.obo $(RELDIR)/basic.obo ;\
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@@ -448,7 +448,8 @@ uberon_sibpair_textmatches(U,A,B,Tok) :-
% for paper:
-aolist(['UBERON','FMA','MA','EMAP','ZFA','XAO','FBbt','WBbt','BTO']).
+%aolist(['CL','FMA','MA','EMAPA','EHDAA2','ZFA','TAO','AAO','XAO','FBbt','WBbt','BTO','PO']).
+aolist(['UBERON','FMA','MA','EMAPA','EHDAA2','ZFA','TAO','AAO','XAO','FBbt','WBbt','BTO','PO','MESH','EFO', ncithesaurus,'NIF_GrossAnatomy']).
% MUST MATCH
@@ -462,7 +463,7 @@ aostat1('Classes',Num,Ont) :- aggregate(count,X,(class(X),id_idspace(X,Ont)),Num
aostat1('Relationships',Num,Ont) :- aggregate(count,X-Y,(parent(X,Y),id_idspace(X,Ont)),Num).
aostat1('Relations',Num,Ont) :- aggregate(count,R,X^Y^(parent(X,R,Y),id_idspace(X,Ont)),Num).
aostat1('% Defined (text)',Pct,Ont) :-
- aggregate(count,D,X^(def(X,D),id_idspace(X,Ont)),Num),
+ aggregate(count,D,X^(class(X),def(X,D),id_idspace(X,Ont)),Num),
pct_classes(Ont,Num,Pct).
aostat1('% Defined (computable)',Pct,Ont) :-
aggregate(count,X,G^(genus(X,G),id_idspace(X,Ont)),Num),
@@ -45,6 +45,10 @@ id: EHDAA2:0004082 ! oropharynx
is_a: UBERON:0001729 ! oropharynx
[Term]
+id: EHDAA2:0004556 ! oropharyngeal cavity
+is_a: UBERON:0009959 ! lumen of oropharynx
+
+[Term]
id: EHDAA2:0004574 ! laryngopharynx
is_a: UBERON:0001051 ! hypopharynx
@@ -881,6 +885,10 @@ id: EHDAA2:0000174 ! bladder
is_a: UBERON:0001255 ! urinary bladder
[Term]
+id: EHDAA2:0004058 ! bladder lumen
+is_a: UBERON:0009958 ! bladder lumen
+
+[Term]
id: EHDAA2:0001367 ! pancreas
is_a: UBERON:0001264 ! pancreas
@@ -1781,6 +1789,10 @@ id: EHDAA2:0000275 ! left atrium
is_a: UBERON:0002079 ! left atrium
[Term]
+id: EHDAA2:0000196 ! right ventricle
+is_a: UBERON:0002080 ! heart right ventricle
+
+[Term]
id: EHDAA2:0002178 ! ventricle
is_a: UBERON:0002082 ! cardiac ventricle
@@ -3073,6 +3085,10 @@ id: EHDAA2:0002135 ! upper limb bud mesenchyme
is_a: UBERON:0003413 ! forelimb bud mesenchyme
[Term]
+id: EHDAA2:0004614 ! tongue mesenchyme
+is_a: UBERON:0003416 ! mesenchyme of tongue
+
+[Term]
id: EHDAA2:0003245 ! chorionic mesenchyme
is_a: UBERON:0003423 ! mesenchyme of chorion
@@ -3321,10 +3337,18 @@ id: EHDAA2:0000141 ! arm muscle system
is_a: UBERON:0001499 ! muscle of arm
[Term]
+id: EHDAA2:0004119 ! tympanic cavity lumen
+is_a: UBERON:0004114 ! tympanic cavity
+
+[Term]
id: EHDAA2:0000738 ! heart
is_a: UBERON:0000948 ! heart
[Term]
+id: EHDAA2:0004162 ! heart mesenchyme
+is_a: UBERON:0009751 ! cardiac mesenchyme
+
+[Term]
id: EHDAA2:0000215 ! myocardial plate
is_a: UBERON:0004139 ! cardiogenic plate
@@ -4945,6 +4969,10 @@ id: EHDAA2:0002098 ! ulna cartilage condensation
is_a: UBERON:0006306 ! ulna cartilage condensation
[Term]
+id: EHDAA2:0004018 ! anal membrane
+is_a: UBERON:0009195 ! anal membrane
+
+[Term]
id: EHDAA2:0002141 ! urogenital membrane
is_a: UBERON:0006307 ! urogenital membrane
@@ -5029,6 +5057,14 @@ id: EHDAA2:0003119 ! epithelial vesicle
is_a: UBERON:0007503 ! epithelial vesicle
[Term]
+id: EHDAA2:0003146 ! dense mesenchymal tissue
+is_a: UBERON:0007524 ! dense mesenchyme tissue
+
+[Term]
+id: EHDAA2:0003151 ! loose mesenchymal tissue
+is_a: UBERON:0007529 ! loose mesenchyme tissue
+
+[Term]
id: EHDAA2:0003152 ! migrating mesenchyme population
is_a: UBERON:0007530 ! migrating mesenchyme population
@@ -947,6 +947,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0000196 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0000196">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002080"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0000196</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0000197 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0000197">
@@ -10501,6 +10510,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0003146 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0003146">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0007524"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0003146</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0003147 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0003147">
@@ -10537,6 +10555,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0003151 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0003151">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0007529"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0003151</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0003152 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0003152">
@@ -10988,6 +11015,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0004018 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004018">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009195"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0004018</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0004020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004020">
@@ -11105,6 +11141,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0004058 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004058">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009958"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0004058</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0004060 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004060">
@@ -11286,6 +11331,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0004119 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004119">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0004114"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0004119</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0004142 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004142">
@@ -11358,6 +11412,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0004162 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004162">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009751"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0004162</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0004183 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004183">
@@ -11557,6 +11620,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0004556 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004556">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009959"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0004556</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0004558 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004558">
@@ -11701,6 +11773,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0004614 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004614">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0003416"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0004614</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0004615 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0004615">
@@ -13753,6 +13834,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0002080 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002080"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_0002082 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002082"/>
@@ -15211,6 +15298,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0003416 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0003416"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_0003421 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0003421"/>
@@ -15583,6 +15676,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0004114 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004114"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_0004128 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004128"/>
@@ -18625,6 +18724,18 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0007524 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0007524"/>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/UBERON_0007529 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0007529"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_0007530 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0007530"/>
@@ -18889,6 +19000,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0009195 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009195"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_0009196 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009196"/>
@@ -19363,6 +19480,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0009751 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009751"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_0009769 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009769"/>
@@ -19402,6 +19525,18 @@
<!-- http://purl.obolibrary.org/obo/UBERON_0009920 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009920"/>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/UBERON_0009958 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009958"/>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/UBERON_0009959 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009959"/>
</rdf:RDF>
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