Integrate deploy perl modules for obo formatted ontologies

pbuttigieg edited this page Sep 7, 2012 · 31 revisions

Tools:

ONTO-perl

Perl-RDF

Use case ontology: http://www.environmentontology.org/

OBO files:

Issue tracker in EnvO repository

Provides feedback and action plan from EnvO team http://code.google.com/p/envo/issues/detail?id=2

Stats:

EnVO basic:

Number of terms: 1557
Number of instances: 0
Number of relationships: 1747
Number of relationships types: 11

EnVO full:

Number of terms: 1778
Number of instances: 0
Number of relationships: 2075
Number of relationships types: 11

Results:

1. date tag value should be updated

current value = date: 25:03:2010 12:49

2. ontology: envo should be ontology:envo

[PLB] See the EnvO Issue related to these results. The OBO appears to be intact [/PLB]

3. superflous synonyms:

[PLB] EA stated that if the term in another vocabulary is syntactically and semantically equivalent, then an xref is more appropriate than a synonym. Also, cases are flagged where the same synonym appears multiple times with different xrefs (e.g. synonym: tidal flat for ENVO: tidal mudflat) rather than listing the xrefs as a list after the one synonym entry.

Some early [feedback] (http://code.google.com/p/envo/issues/detail?id=2) from the EnvO team notes that this is largely a stylistic issue. Further, many of the terms below belong to CHEBI and are present due to the MIREOTing process. [/PLB]

  • synonym: "primary alcohol" EXACT [IntEnz:NULL]
  • synonym: "pantothenate" EXACT [IntEnz:NULL]
  • synonym: "lipid" EXACT [IntEnz:NULL]
  • synonym: "arsenic molecular entity" EXACT [ChEBI:NULL]
  • synonym: "chromium molecular entity" EXACT [ChEBI:NULL]
  • synonym: "oxide" EXACT [ChEBI:NULL]
  • synonym: "oxygen molecular entity" EXACT [ChEBI:NULL]
  • synonym: "monocarboxylic acid amide" EXACT [IntEnz:NULL]
  • synonym: "salicylate" EXACT [IntEnz:NULL]
  • synonym: "alcohol" EXACT [IntEnz:NULL]
  • synonym: "primary amide" EXACT [IUPAC:NULL]
  • synonym: "pnictogen molecular entity" EXACT [ChEBI:NULL]
  • synonym: "chalcogen molecular entity" EXACT [ChEBI:NULL]
  • synonym: "pnictogen oxoanion" EXACT [ChEBI:NULL]
  • synonym: "carbon group molecular entity" EXACT [ChEBI:NULL]
  • synonym: "cyclic hydrocarbon" EXACT [ChEBI:NULL]
  • synonym: "s-block molecular entity" EXACT [ChEBI:NULL]
  • synonym: "d-block molecular entity" EXACT [ChEBI:NULL]
  • synonym: "chromium group molecular entity" EXACT [ChEBI:NULL]
  • synonym: "chromium oxoanion" EXACT [ChEBI:NULL]
  • synonym: "oxoanion" EXACT [ChEBI:NULL]
  • synonym: "ortho-fused bicyclic arene" EXACT [ChEBI:NULL]
  • synonym: "ortho-fused polycyclic hydrocarbon" EXACT [ChEBI:NULL]
  • synonym: "ortho-fused bicyclic hydrocarbon" EXACT [ChEBI:NULL]
  • synonym: "arsenic oxoanion" EXACT [ChEBI:NULL]
  • synonym: "organochalcogen compound" EXACT [ChEBI:NULL]
  • synonym: "organooxygen compound" EXACT [ChEBI:NULL]
  • synonym: "methylindole" EXACT [ChEBI:NULL]
  • synonym: "alkylbenzene" EXACT [ChEBI:NULL]
  • synonym: "garden" EXACT [Geonames:feature]
  • synonym: "canal" EXACT [Geonames:feature]
  • synonym: "ocean" EXACT [Geonames:feature]
  • synonym: "sea" EXACT [Geonames:feature]
  • synonym: "sea" EXACT [ADL:FTT]
  • synonym: "salt lake" EXACT [Getty:TGN]
  • synonym: "salt lake" EXACT [USGS:SDTS]
  • synonym: "lake" EXACT [Geonames:feature]
  • synonym: "rio" EXACT [USGS:SDTS]
  • synonym: "stream" EXACT [Geonames:feature]
  • synonym: "intermittent stream" EXACT [Geonames:feature]
  • synonym: "reservoir" EXACT [Geonames:feature]
  • synonym: "well" EXACT [Geonames:feature]
  • synonym: "spring" EXACT [Geonames:feature]
  • synonym: "watercourse" EXACT [Geonames:feature]
  • synonym: "wadi" EXACT [Geonames:feature]
  • synonym: "rapids" EXACT [Geonames:feature]
  • synonym: "rapids" EXACT [ADL:FTT]
  • synonym: "irrigation canal" EXACT [ADL:FTT]
  • synonym: "irrigation canal" EXACT [Geonames:feature]
  • synonym: "ditch" EXACT [Geonames:feature]
  • synonym: "ditch" EXACT [ADL:FTT]
  • synonym: "lagoon" EXACT [Geonames:feature]
  • synonym: "laguna" EXACT [ADL:FTT]
  • synonym: "fiord" EXACT [NASA:earthrealm]
  • synonym: "fjord" EXACT [Geonames:feature]
  • synonym: "tidal creek" EXACT [Geonames:feature]
  • synonym: "drainage canal" EXACT [ADL:FTT]
  • synonym: "drainage canal" EXACT [Geonames:feature]
  • synonym: "wetland" EXACT [Geonames:feature]
  • synonym: "estuary" EXACT [Geonames:feature]
  • synonym: "navigation canal" EXACT [Geonames:feature]
  • synonym: "navigation channel" EXACT [Geonames:feature]
  • synonym: "geyser" EXACT [Geonames:feature]
  • synonym: "hot spring" EXACT [Geonames:feature]
  • synonym: "crater lake" EXACT [Geonames:feature]
  • synonym: "salt marsh" EXACT [USGS:SDTS]
  • synonym: "salt evaporation pond" EXACT [ADL:FTT]
  • synonym: "mangrove swamp" EXACT [Geonames:feature]
  • synonym: "underground lake" EXACT [Geonames:feature]
  • synonym: "populated place" EXACT [Geonames:feature]
  • synonym: "body of water" EXACT [Getty:TGN]
  • synonym: "road" EXACT [Geonames:feature]
  • synonym: "railroad" EXACT [USGS:SDTS]
  • synonym: "railroad" EXACT [Geonames:feature]
  • synonym: "tunnel" EXACT [Geonames:feature]
  • synonym: "distributary" EXACT [ADL:FTT]
  • synonym: "distributary" EXACT [Geonames:feature]
  • synonym: "aqueduct" EXACT [Geonames:feature]
  • synonym: "aqueduct" EXACT [Getty:TGN]
  • synonym: "building" EXACT [Geonames:feature]
  • synonym: "dam" EXACT [Geonames:feature]
  • synonym: "bridge" EXACT [Geonames:feature]
  • synonym: "pass" EXACT [Geonames:feature]
  • synonym: "plain" EXACT [Geonames:feature]
  • synonym: "cliff" EXACT [Geonames:feature]
  • synonym: "lava area" EXACT [Geonames:feature]
  • synonym: "caldera" EXACT [Geonames:feature]
  • synonym: "desert" EXACT [Geonames:feature]
  • synonym: "island" EXACT [Geonames:feature]
  • synonym: "artificial island" EXACT [Geonames:feature]
  • synonym: "valley" EXACT [Geonames:feature]
  • synonym: "delta" EXACT [Geonames:feature]
  • synonym: "mangrove island" EXACT [Geonames:feature]
  • synonym: "grassland" EXACT [Geonames:feature]
  • synonym: "heath" EXACT [Geonames:feature]
  • synonym: "meadow" EXACT [Geonames:feature]
  • synonym: "tundra" EXACT [Geonames:feature]
  • synonym: "field" EXACT [Geonames:feature]
  • synonym: "orchard" EXACT [Geonames:feature]
  • synonym: "vineyard" EXACT [Geonames:feature]
  • synonym: "oil palm plantation" EXACT [Geonames:feature]
  • synonym: "glacier" EXACT [Geonames:feature]
  • synonym: "buffer zone" EXACT [Geonames:feature]
  • synonym: "neutral zone" EXACT [ADL:FTT]
  • synonym: "irrigation ditch" EXACT [ADL:FTT]
  • synonym: "irrigation ditch" EXACT [Geonames:feature]
  • synonym: "drainage ditch" EXACT [Geonames:feature]
  • synonym: "drainage ditch" EXACT [ADL:FTT]
  • synonym: "stream bank" EXACT [Geonames:feature]
  • synonym: "icecap" EXACT [Geonames:feature]
  • synonym: "snowfield" EXACT [Getty:TGN]
  • synonym: "ocean current" EXACT [ADL:FTT]
  • synonym: "coral reef" EXACT [ADL:FTT]
  • synonym: "coral reef" EXACT [Geonames:feature]
  • synonym: "coral reef" EXACT [USGS:SDTS]
  • synonym: "sabkha" EXACT [Geonames:feature]
  • synonym: "anabranch" EXACT [Geonames:feature]
  • synonym: "cirque" EXACT [Geonames:feature]
  • synonym: "oasis" EXACT [Geonames:feature]
  • synonym: "sugar plantation" EXACT [Geonames:feature]
  • synonym: "sisal plantation" EXACT [Geonames:feature]
  • synonym: "banana plantation" EXACT [Geonames:feature]
  • synonym: "tea plantation" EXACT [Geonames:feature]
  • synonym: "rubber plantation" EXACT [Geonames:feature]
  • synonym: "asphalt lake" EXACT [Geonames:feature]
  • synonym: "atoll" EXACT [Geonames:feature]
  • synonym: "blowhole" EXACT [Geonames:feature]
  • synonym: "dune" EXACT [Geonames:feature]
  • synonym: "sandy desert" EXACT [Geonames:feature]
  • synonym: "isthmus" EXACT [Geonames:feature]
  • synonym: "karst" EXACT [Geonames:feature]
  • synonym: "moraine" EXACT [Geonames:feature]
  • synonym: "mesa" EXACT [Geonames:feature]
  • synonym: "stony desert" EXACT [Geonames:feature]
  • synonym: "hanging valley" EXACT [Geonames:feature]
  • synonym: "mud flat" EXACT [ADL:FTT]
  • synonym: "oxbow lake" EXACT [Geonames:feature]
  • synonym: "swamp" EXACT [Geonames:feature]
  • synonym: "tidal flat" EXACT [USGS:SDTS]
  • synonym: "tidal flat" EXACT [ADL:FTT]
  • synonym: "volcano" EXACT [Geonames:feature]
  • synonym: "seamount" EXACT [Geonames:feature]
  • synonym: "confluence" EXACT [ADL:FTT]
  • synonym: "confluence" EXACT [Geonames:feature]
  • synonym: "continental rise" EXACT [Geonames:feature]
  • synonym: "ocean trench" EXACT [ADL:FTT]
  • synonym: "escarpment" EXACT [Geonames:feature]
  • synonym: "quarry" EXACT [Geonames:feature]
  • synonym: "quicksand" EXACT [Geonames:feature]
  • synonym: "polder" EXACT [Geonames:feature]
  • synonym: "butte" EXACT [Geonames:feature]
  • synonym: "cotton plantation" EXACT [Geonames:feature]
  • synonym: "divide" EXACT [Geonames:feature]
  • synonym: "scrubland" EXACT [Geonames:feature]
  • synonym: "coast" EXACT [Geonames:feature]
  • synonym: "shore" EXACT [Geonames:feature]
  • synonym: "peninsula" EXACT [Geonames:feature]
  • synonym: "interdune trough" EXACT [Geonames:feature]
  • synonym: "blowout" EXACT [Geonames:feature]
  • synonym: "icecap dome" EXACT [Geonames:feature]
  • synonym: "stream bed" EXACT [Geonames:feature]
  • synonym: "stream mouth" EXACT [Geonames:feature]
  • synonym: "intermittent lake" EXACT [Geonames:feature]
  • synonym: "intermittent wetland" EXACT [Geonames:feature]
  • synonym: "sound" EXACT [Geonames:feature]
  • synonym: "strait" EXACT [Geonames:feature]
  • synonym: "sea channel" EXACT [Geonames:feature]
  • synonym: "ford" EXACT [USGS:SDTS]
  • synonym: "clearing" EXACT [Geonames:feature]
  • synonym: "inlet" EXACT [Geonames:feature]
  • synonym: "peak" EXACT [Geonames:feature]
  • synonym: "intermittent oxbow lake" EXACT [Geonames:feature]
  • synonym: "intermittent pond" EXACT [Geonames:feature]
  • synonym: "intermittent pool" EXACT [Geonames:feature]
  • synonym: "underground irrigation canal" EXACT [Geonames:feature]
  • synonym: "underground irrigation canal" EXACT [ADL:FTT]
  • synonym: "intermittent reservoir" EXACT [Geonames:feature]
  • synonym: "wadi mouth" EXACT [Geonames:feature]
  • synonym: "meander neck" EXACT [Geonames:feature]
  • synonym: "road cut" EXACT [Geonames:feature]
  • synonym: "ditch mouth" EXACT [ADL:FTT]
  • synonym: "ditch mouth" EXACT [Geonames:feature]
  • synonym: "rockfall" EXACT [Geonames:feature]
  • synonym: "canal tunnel" EXACT [Geonames:feature]
  • synonym: "abandoned watercourse" EXACT [Geonames:feature]
  • synonym: "canalized stream" EXACT [Geonames:feature]
  • synonym: "interfluve" EXACT [Geonames:feature]
  • synonym: "beach ridge" EXACT [Geonames:feature]
  • synonym: "apron" EXACT [Geonames:feature]
  • synonym: "icecap depression" EXACT [ADL:FTT]
  • synonym: "intermittent salt pond" EXACT [ADL:FTT]
  • synonym: "weir" EXACT [Geonames:feature]
  • synonym: "moatan" EXACT [Geonames:feature]
  • synonym: "boulder field" EXACT [Geonames:feature]
  • synonym: "arrugado" EXACT [Geonames:feature]
  • synonym: "arrugado" EXACT [ADL:FTT]
  • synonym: "water hole" EXACT []

4. Names should be reviewed (check the use of keywords such as OR)

[PLB] Note: Most if not all of these biome names are from their native classification schemes (Bailey, Udvardy, WWF). There are some efforts to develop a more homogenous representation of these categories which would omit these keywords, although the time to implementation is unclear at the moment. [/PLB]

  • ENVO:00002987 Evergreen sclerophyllous forests, scrub, or woodlands
  • ENVO:00002989 Temperate broad-leaf forests or woodlands and subpolar deciduous thickets
  • ENVO:00002990 Tropical dry or deciduous forests (including Monsoon forests) or woodlands
  • ENVO:00002991 Subtropical and temperate rainforests or woodlands
  • ENVO:00002992 Temperate needle-leaf forests or woodlands

5. Names should be reviewed (check the use of keywords such as AND)

[PLB] Note: Most if not all of these biome names are from their native classification schemes (Bailey, Udvardy, WWF). There are some efforts to develop a more homogenous representation of these categories which would omit these keywords, although the time to implementation is unclear at the moment.[/PLB]

  • ENVO:00000876 Temperate broadleaf and mixed forest biome
  • ENVO:00000877 Temperate grasslands, savannas, and shrubland biome
  • ENVO:00000878 Mediterranean forests, woodlands, and shrub biome
  • ENVO:00000879 Tropical and subtropical moist broadleaf forest biome
  • ENVO:00000880 Tropical and subtropical dry broadleaf forest biome
  • ENVO:00000881 Tropical and subtropical grasslands, savannas, and shrubland biome
  • ENVO:00000882 Montane grasslands and shrubland biome
  • ENVO:00000883 Deserts and xeric shrubland biome
  • ENVO:00000885 Flooded grasslands and savanna biome
  • ENVO:00000895 Temperate shelf and sea biome
  • ENVO:00002989 Temperate broad-leaf forests or woodlands and subpolar deciduous thickets
  • ENVO:00002991 Subtropical and temperate rainforests or woodlands
  • ENVO:00002995 Tundra communities and barren Arctic deserts
  • ENVO:00002996 Mixed mountain and highland systems with complex zonation
  • ENVO:00002997 Cold-winter (continental) deserts and semideserts
  • ENVO:00002998 Warm deserts and semideserts
  • ENVO:00005806 Tropical and subtropical coniferous forest biome

6. Possible superflous relationships (transitive reduction, multiple inheritance)

[PLB]This will be fixed.[?PLB]

check relationship: part_of ENVO:00000029 ! watercourse

in entry:

[Term]
id: ENVO:00002127
name: stream sediment
is_a: ENVO:00002007 ! sediment
relationship: part_of ENVO:00000022 ! river
relationship: part_of ENVO:00000029 ! watercourse

"visually":

stream sediment  ----part_of---> river ----is_a---> stream ----is_a---> watercourse
   |                                                                        ^
   |                                                                        |
   |-------------------------------------part_of----------------------------|

a better image (https://www.dropbox.com/s/o2addgdc14rpg8a/EnVO2.png) which is not displayed ;-) :

Superflous relation in EnVO

check:

is_a: ENVO:00000086 ! plain

and

is_a: ENVO:00000175 ! karst

in entry:

[Term]
id: ENVO:00004683
name: karst field
def: "A large flat plain in karst territory with areas usually 5 to 400 km2." [Wikipedia:Karst_field]
xref: Wikipedia:Karst_field
is_a: ENVO:00000086 ! plain
is_a: ENVO:00000175 ! karst
relationship: located_in ENVO:00000175 ! karst

7. Defined subsets (in envo-basic.obo) BUT not used anywhere!

[PLB] Early feedback from the EnvO team reports that these subset defs arose from OORT MIREOTing process. This will be reported to OORT. [/PLB]

subsetdef: abnormal_slim "Abnormal/normal slim"
subsetdef: absent_slim "Absent/present slim"
subsetdef: attribute_slim "Attribute slim"
subsetdef: cell_quality "cell_quality"
subsetdef: relational_slim "Relational slim: types of quality that require an additional entity in order to exist"
subsetdef: value_slim "Value slim"

8. RDF transformations (obo2rdf) of the Environmental Ontology

EnVO basic: https://www.dropbox.com/s/b7ggt09xubqe5t8/envo_basic.rdf

EnVO basic - transitive closure: https://www.dropbox.com/s/n25p1w6muunx70v/envo_basic_tc.rdf

EnVO full: https://www.dropbox.com/s/fc4mkrdj5h0haik/envo.rdf

EnVO full - transitive closure: https://www.dropbox.com/s/yh5qx3vshh5l2bj/envo_tc.rdf

You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.