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First pass at mining DPs from existing PO ldefs. Issue #662
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@cmungall
cmungall committed Feb 13, 2017
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25 changes: 25 additions & 0 deletions Makefile
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Expand Up @@ -52,3 +52,28 @@ mirror/%.owl: $(SRC)
mirror/ncbitaxon.owl:
$(OWLTOOLS) $(OBO)/ncbitaxon/subsets/taxslim.obo --remove-annotation-assertions -l -s -d --remove-dangling-annotations --set-ontology-id $(OBO)/ncbitaxon -o $@
.PRECIOUS: mirror/ncbitaxon.owl

# ----------------------------------------
# MINING DEAD SIMPLE DESIGN PATTERNS
# ----------------------------------------
MODDIR=modules
PATTERNDIR=patterns

#MODS = luminal_space_of gland_duct gland_acinus endochondral_bone endochondral_cartilage
MODS = cortex

# OWL->CSV
PSRC = plant-ontology.obo

# reverse engineer CSV from uberon axioms and DOSDPs
modules/%-ldef.csv: $(PSRC)
blip-findall -debug odp -i $< -u odputil -i $(PATTERNDIR)/po_patterns.pro "write_tuple($*)" > $@.tmp && mv $@.tmp $@
.PRECIOUS: modules/%.csv
modules/%-lex.csv: $(PSRC)
blip-findall -debug odp -i $< -u odputil -i $(PATTERNDIR)/po_patterns.pro "write_tuple_lex($*)" > $@.tmp && mv $@.tmp $@
.PRECIOUS: modules/%.csv

# currently, the pattern source is prolog - generate dosdp yaml from this
$(PATTERNDIR)/%.yaml: patterns/po_patterns.pro
blip-findall -i $(PSRC) -u odputil -i $(PATTERNDIR)/po_patterns.pro "write_yaml($*),fail" > $@.tmp && mv $@.tmp $@
.PRECIOUS: $(PATTERNDIR)/%.yaml
77 changes: 77 additions & 0 deletions modules/part_whole.csv
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iri,label,part,part label,whole,whole label
PO:0004525,"secondary xylem parenchyma cell",PO:0000074,"parenchyma cell",PO:0004532,"secondary xylem parenchyma"
PO:0025179,"branch epidermis",PO:0000112,"shoot axis epidermis",PO:0025073,"branch"
PO:0009106,"tassel meristem",PO:0000230,"inflorescence meristem",PO:0020126,"tassel inflorescence"
PO:0009109,"ear meristem",PO:0000230,"inflorescence meristem",PO:0020136,"ear inflorescence"
PO:0025455,"primary phloem sieve tube element",PO:0000289,"sieve tube element",PO:0006075,"primary phloem"
PO:0025457,"secondary phloem sieve tube element",PO:0000289,"sieve tube element",PO:0005043,"secondary phloem"
PO:0025445,"secondary xylem tracheary element",PO:0000290,"tracheary element",PO:0005848,"secondary xylem"
PO:0025461,"early wood tracheary element",PO:0000290,"tracheary element",PO:0004515,"early wood"
PO:0025462,"late wood tracheary element",PO:0000290,"tracheary element",PO:0004516,"late wood"
PO:0025447,"secondary xylem tracheid",PO:0000301,"tracheid",PO:0005848,"secondary xylem"
PO:0025448,"primary xylem vessel member",PO:0002003,"xylem vessel member",PO:0005849,"primary xylem"
PO:0025449,"secondary xylem vessel member",PO:0002003,"xylem vessel member",PO:0005848,"secondary xylem"
PO:0004526,"axial secondary xylem parenchyma cell",PO:0004525,"secondary xylem parenchyma cell",PO:0004533,"axial secondary xylem parenchyma"
PO:0004527,"ray secondary xylem parenchyma cell",PO:0004525,"secondary xylem parenchyma cell",PO:0004534,"ray secondary xylem parenchyma"
PO:0004533,"axial secondary xylem parenchyma",PO:0004532,"secondary xylem parenchyma",PO:0025410,"axial system"
PO:0004534,"ray secondary xylem parenchyma",PO:0004532,"secondary xylem parenchyma",PO:0025411,"ray system"
PO:0025348,"phyllome lamina vein",PO:0005020,"vascular bundle",PO:0025396,"phyllome lamina"
PO:0004532,"secondary xylem parenchyma",PO:0005421,"parenchyma",PO:0005848,"secondary xylem"
PO:0006035,"shoot system epidermis",PO:0005679,"epidermis",PO:0009006,"shoot system"
PO:0006036,"root epidermis",PO:0005679,"epidermis",NCBITaxon:1,
PO:0006043,"integument epidermis",PO:0005679,"epidermis",PO:0020021,"integument"
PO:0006048,"seed coat epidermis",PO:0005679,"epidermis",PO:0009088,"seed coat"
PO:0006063,"plant ovary epidermis",PO:0005679,"epidermis",PO:0005022,"plant ovary wall"
PO:0030073,"exothecium",PO:0005679,"epidermis",PO:0025306,"sporangium wall"
PO:0000047,"leaf lamina epidermis",PO:0006016,"leaf epidermis",PO:0020039,"leaf lamina"
PO:0000051,"petiole epidermis",PO:0006016,"leaf epidermis",PO:0020038,"petiole"
PO:0025249,"leaf sheath epidermis",PO:0006016,"leaf epidermis",PO:0020104,"leaf sheath"
PO:0000112,"shoot axis epidermis",PO:0006035,"shoot system epidermis",PO:0025029,"shoot axis"
PO:0000207,"nectary epidermis",PO:0006035,"shoot system epidermis",PO:0009035,"nectary"
PO:0006049,"scutellum epidermis",PO:0006035,"shoot system epidermis",PO:0020110,"scutellum"
PO:0025157,"phyllome epidermis",PO:0006035,"shoot system epidermis",PO:0006001,"phyllome"
PO:0006039,"shoot-borne root epidermis",PO:0006036,"root epidermis",PO:0000042,"shoot-borne root"
PO:0025233,"portion of embryo plant tissue",PO:0009007,"portion of plant tissue",PO:0009009,"plant embryo"
PO:0025395,"floral organ",PO:0009008,"plant organ",PO:0009046,"flower"
PO:0025099,"embryo plant structure",PO:0009011,"plant structure",PO:0009009,"plant embryo"
PO:0006367,"glume of ear spikelet",PO:0009039,"glume",PO:0006320,"ear spikelet"
PO:0006368,"glume of tassel spikelet",PO:0009039,"glume",PO:0006309,"tassel spikelet"
PO:0008005,"fruit nucellus",PO:0020020,"nucellus",PO:0009001,"fruit"
PO:0025018,"phyllome margin",PO:0025005,"plant organ margin",PO:0025396,"phyllome lamina"
PO:0020128,"leaf margin",PO:0025018,"phyllome margin",PO:0025034,"leaf"
PO:0030020,"gametophore axis",PO:0025029,"shoot axis",PO:0030018,"gametophore"
PO:0025056,"aerial tuber cortex",PO:0025055,"tuber cortex",PO:0025039,"aerial tuber storage parenchyma"
PO:0025057,"subterranean tuber cortex",PO:0025055,"tuber cortex",PO:0025038,"subterranean tuber storage parenchyma"
PO:0025129,"petiole lamina",PO:0025060,"lamina",PO:0020038,"petiole"
PO:0025513,"plant organ lamina",PO:0025060,"lamina",PO:0009008,"plant organ"
PO:0006060,"filament epidermis",PO:0025097,"stamen epidermis",PO:0009067,"filament"
PO:0006016,"leaf epidermis",PO:0025157,"phyllome epidermis",PO:0025034,"leaf"
PO:0006040,"sepal epidermis",PO:0025157,"phyllome epidermis",PO:0009031,"sepal"
PO:0006041,"petal epidermis",PO:0025157,"phyllome epidermis",PO:0009032,"petal"
PO:0025096,"carpel epidermis",PO:0025157,"phyllome epidermis",PO:0009030,"carpel"
PO:0025097,"stamen epidermis",PO:0025157,"phyllome epidermis",PO:0009029,"stamen"
PO:0025158,"bract epidermis",PO:0025157,"phyllome epidermis",PO:0009055,"bract"
PO:0025184,"tepal epidermis",PO:0025157,"phyllome epidermis",PO:0009033,"tepal"
PO:0025178,"stem epidermis",PO:0025178,"stem epidermis",PO:0020100,"hypocotyl"
PO:0025380,"leaf mesophyll intercellular space",PO:0025379,"intercellular space",PO:0005645,"leaf mesophyll"
PO:0025392,"leaf lamina areole",PO:0025391,"phyllome lamina areole",PO:0020039,"leaf lamina"
PO:0025452,"primary phloem sieve element",PO:0025406,"sieve element",PO:0006075,"primary phloem"
PO:0025453,"secondary phloem sieve element",PO:0025406,"sieve element",PO:0005043,"secondary phloem"
PO:0000274,"xylem fiber cell",PO:0025407,"plant fiber cell",PO:0005352,"xylem"
PO:0004519,"phloem fiber cell",PO:0025407,"plant fiber cell",PO:0005417,"phloem"
PO:0025442,"stem secondary thickening meristem",PO:0025414,"secondary thickening meristem",PO:0009047,"stem"
PO:0025443,"root secondary thickening meristem",PO:0025414,"secondary thickening meristem",PO:0009005,"root"
PO:0025454,"primary phloem sieve cell",PO:0025415,"sieve cell",PO:0006075,"primary phloem"
PO:0025456,"secondary phloem sieve cell",PO:0025415,"sieve cell",PO:0005043,"secondary phloem"
PO:0025450,"primary xylem vessel",PO:0025417,"xylem vessel",PO:0005849,"primary xylem"
PO:0025451,"secondary xylem vessel",PO:0025417,"xylem vessel",PO:0005848,"secondary xylem"
PO:0025440,"shoot axis cambial zone",PO:0025439,"cambial zone",PO:0025029,"shoot axis"
PO:0025441,"root cambial zone",PO:0025439,"cambial zone",PO:0009005,"root"
PO:0025001,"cardinal organ part",PO:0025498,"cardinal part of multi-tissue plant structure",PO:0009008,"plant organ"
PO:0025396,"phyllome lamina",PO:0025513,"plant organ lamina",PO:0006001,"phyllome"
PO:0025517,"leaf lamina lobe",PO:0025514,"phyllome lamina lobe",PO:0025034,"leaf"
PO:0025518,"leaf lamina tooth",PO:0025515,"phyllome lamina tooth",PO:0025034,"leaf"
PO:0025519,"leaf lamina crena",PO:0025516,"phyllome lamina crena",PO:0025034,"leaf"
PO:0025026,"embryo sac cell",PO:0025606,"native plant cell",PO:0025074,"embryo sac"
PO:0025028,"embryo plant cell",PO:0025606,"native plant cell",PO:0009009,"plant embryo"
PO:0030019,"gametophore meristematic apical cell",PO:0030009,"shoot meristematic apical cell",PO:0030018,"gametophore"
37 changes: 37 additions & 0 deletions patterns/part_whole.yaml
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pattern_name: part_whole

classes: []

relations:
part_of: BFO:0000050

vars:
part: "Thing"
whole: "Thing"

name:
text: "%s %s"
vars:
- whole
- part

annotations:
- property: oio:hasExactSynonym
text: "%s of %s"
vars:
- part
- whole

def:
text: "A portion of %s that is part of a %s."
vars:
- part
- whole

equivalentTo:
text: "%s and 'part_of' some %s"
vars:
- part
- whole


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