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review robot report 2020-09-30 #1018

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wdduncan opened this issue Sep 30, 2020 · 7 comments
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review robot report 2020-09-30 #1018

wdduncan opened this issue Sep 30, 2020 · 7 comments
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@wdduncan
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wdduncan commented Sep 30, 2020 •
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I ran the robot report on http://purl.obolibrary.org/obo/envo/releases/2020-06-10/envo.owl.
Summary of results are:

Violations: 2067
-----------------
ERROR:      39
WARN:       1887
INFO:       141

The command to produce the report is:

robot report -i envo.owl \
  --labels true \
  --tdb true \
  --fail-on none \
  -o envo-report-2020-09-20.tsv

Zip file of the TSV output attached.
envo-report-2020-09-20.tsv.gz

For easier viewing, I am also attaching the zip of the html output.
envo-report-2020-09-20.html.gz

cc @cmungall @pbuttigieg
@wdduncan wdduncan mentioned this issue Sep 30, 2020
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@wdduncan
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See https://douroucouli.wordpress.com/2019/03/03/checking-ontologies-using-robot-report-with-an-example-from-the-cephalopod-ontology/

First we need to eliminate all ERRORs, we should also take a look at WARNings. Some of these are pipeline issues, e.g lack of labels for imports, I will take a look at these.

See also ticket #700

@cmungall
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cmungall commented Oct 2, 2020

summarizing errors; good news, these are all from imports:

egrep -v '^(WARN|INFO)' envo-report-2020-09-20.tsv | tbl2ghwiki

Level Rule Name Subject Property Value
ERROR missing_label IAO:0000004 rdfs:label
ERROR deprecated_class_reference obsolete: plant [FOODON:03411347] rdfs:subClassOf plant used for producing extract or concentrate [FOODON:03411013]
ERROR deprecated_class_reference obsolete: plant [FOODON:03411347] rdfs:subClassOf fruit-producing plant [FOODON:03411140]
ERROR deprecated_class_reference obsolete: plant [FOODON:03411347] rdfs:subClassOf plant according to family [FOODON:03413357]
ERROR duplicate_label root [NCBITaxon:1] rdfs:label root
ERROR duplicate_label root [PO:0009005] rdfs:label root
ERROR duplicate_label primordium [PO:0025127] rdfs:label primordium
ERROR duplicate_label primordium [UBERON:0001048] rdfs:label primordium
ERROR duplicate_label organ [ENVO:01000162] rdfs:label organ
ERROR duplicate_label organ [UBERON:0000062] rdfs:label organ
ERROR duplicate_label mouth [ENVO:00000479] rdfs:label mouth
ERROR duplicate_label mouth [UBERON:0000165] rdfs:label mouth
ERROR duplicate_label elevation [ENVO:00000176] rdfs:label elevation
ERROR duplicate_label elevation [PATO:0001687] rdfs:label elevation
ERROR multiple_definitions independent continuant [BFO:0000004] definition [IAO:0000115] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.@en
ERROR multiple_definitions independent continuant [BFO:0000004] definition [IAO:0000115] b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])@en
ERROR multiple_definitions process [BFO:0000015] definition [IAO:0000115] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.@en
ERROR multiple_definitions process [BFO:0000015] definition [IAO:0000115] p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])@en
ERROR multiple_definitions specifically dependent continuant [BFO:0000020] definition [IAO:0000115] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.@en
ERROR multiple_definitions specifically dependent continuant [BFO:0000020] definition [IAO:0000115] b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en
ERROR multiple_definitions specifically dependent continuant [BFO:0000020] definition [IAO:0000115] b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en
ERROR multiple_definitions generically dependent continuant [BFO:0000031] definition [IAO:0000115] A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.@en
ERROR multiple_definitions generically dependent continuant [BFO:0000031] definition [IAO:0000115] b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])@en
ERROR multiple_definitions yogurt food product [FOODON:00001014] definition [IAO:0000115] A dairy product produced by bacterial fermentation of milk.@en
ERROR multiple_definitions yogurt food product [FOODON:00001014] definition [IAO:0000115] Yogurt is a food produced by bacterial fermentation of milk. The bacteria used to make yogurt are known as yogurt cultures. The fermentation of lactose by these bacteria produces lactic acid, which acts on milk protein to give yogurt its texture and characteristic tart flavor.@en
ERROR multiple_labels fiat object part [BFO:0000024] rdfs:label fiat object@en
ERROR multiple_labels fiat object part [BFO:0000024] rdfs:label fiat object part@en
ERROR multiple_labels mollusk food product [FOODON:00002044] rdfs:label mollusc food product@en
ERROR multiple_labels mollusk food product [FOODON:00002044] rdfs:label mollusk food product@en-us
ERROR multiple_labels temporal interpretation [RO:0001900] rdfs:label temporal interpretation
ERROR multiple_labels temporal interpretation [RO:0001900] rdfs:label temporal interpretation@en
ERROR multiple_labels connects [RO:0002176] rdfs:label connects
ERROR multiple_labels connects [RO:0002176] rdfs:label connects@en
ERROR multiple_labels regulates [RO:0002211] rdfs:label regulates@en
ERROR multiple_labels regulates [RO:0002211] rdfs:label regulates (processual)
ERROR multiple_labels surrounded by [RO:0002219] rdfs:label surrounded by
ERROR multiple_labels surrounded by [RO:0002219] rdfs:label surrounded by@en
ERROR multiple_labels has habitat [RO:0002303] rdfs:label has habitat
ERROR multiple_labels has habitat [RO:0002303] rdfs:label has habitat@en

@cmungall
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cmungall commented Oct 2, 2020

good news, no failures on envo-base:

$ robot report -i ../../envo-base.owl   --labels true   --tdb true   --fail-on error   -o envo-base-report-2020-09-20.tsv
Violations: 596
-----------------
ERROR:      0
WARN:       385
INFO:       211

We should switch the makefile such that we fail on errors in base from here on

Summary: (cut -f1,2 envo-base-report-2020-09-20.tsv | count-occ.pl | mysort -k 1 -n -r)

1 Level Rule Name
340 WARN missing_definition
190 INFO missing_superclass
41 WARN duplicate_scoped_synonym
21 INFO lowercase_definition
3 WARN annotation_whitespace
1 WARN invalid_xref

@cmungall
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cmungall commented Oct 2, 2020

We should turn invalid_xref into ERROR

Need to fix this:

WARN    invalid_xref    material primarily composed of biogenic carbonates [ENVO:01001644]      database_cross_reference [oboInOwl:hasDbXref]   Carbonate which is formed as the result of some biological process.

missing_superclass obviously false positives for base

we should aim to get down the missing defs

@cmungall
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cmungall commented Oct 5, 2020 •
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Something is not right

report should be telling us things like the fact that thermokast formation process has the same exact syn as a different class 'thermokarst'

UPDATE no such check in robot. Will add: ontodev/robot#747

@cmungall
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cmungall commented Oct 5, 2020

We should fix these

level duplicate_scoped_synonym term scope syn
WARN duplicate_scoped_synonym watercourse [ENVO:00000029] has_narrow_synonym [oboInOwl:hasNarrowSynonym] narrows
WARN duplicate_scoped_synonym watercourse [ENVO:00000029] has_related_synonym [oboInOwl:hasRelatedSynonym] narrows
WARN duplicate_scoped_synonym pond [ENVO:00000033] has_narrow_synonym [oboInOwl:hasNarrowSynonym] pool (water body)
WARN duplicate_scoped_synonym pond [ENVO:00000033] has_related_synonym [oboInOwl:hasRelatedSynonym] pool (water body)
WARN duplicate_scoped_synonym navigation canal [ENVO:00000048] has_exact_synonym [oboInOwl:hasExactSynonym] navigation canal
WARN duplicate_scoped_synonym navigation canal [ENVO:00000048] has_exact_synonym [oboInOwl:hasExactSynonym] navigation channel
WARN duplicate_scoped_synonym navigation canal [ENVO:00000048] has_narrow_synonym [oboInOwl:hasNarrowSynonym] navigation canal
WARN duplicate_scoped_synonym navigation canal [ENVO:00000048] has_related_synonym [oboInOwl:hasRelatedSynonym] navigation channel
WARN duplicate_scoped_synonym saline marsh [ENVO:00000054] has_exact_synonym [oboInOwl:hasExactSynonym] salt marsh
WARN duplicate_scoped_synonym saline marsh [ENVO:00000054] has_related_synonym [oboInOwl:hasRelatedSynonym] salt marsh
WARN duplicate_scoped_synonym mountain pass [ENVO:00000084] has_exact_synonym [oboInOwl:hasExactSynonym] pass
WARN duplicate_scoped_synonym mountain pass [ENVO:00000084] has_related_synonym [oboInOwl:hasRelatedSynonym] pass
WARN duplicate_scoped_synonym snow field [ENVO:00000146] has_exact_synonym [oboInOwl:hasExactSynonym] snowfield
WARN duplicate_scoped_synonym snow field [ENVO:00000146] has_related_synonym [oboInOwl:hasRelatedSynonym] snowfield
WARN duplicate_scoped_synonym atoll [ENVO:00000166] has_exact_synonym [oboInOwl:hasExactSynonym] atoll
WARN duplicate_scoped_synonym atoll [ENVO:00000166] has_related_synonym [oboInOwl:hasRelatedSynonym] atoll
WARN duplicate_scoped_synonym mudflat [ENVO:00000192] has_exact_synonym [oboInOwl:hasExactSynonym] mud flat
WARN duplicate_scoped_synonym mudflat [ENVO:00000192] has_related_synonym [oboInOwl:hasRelatedSynonym] mud flat
WARN duplicate_scoped_synonym bayou [ENVO:00000234] has_broad_synonym [oboInOwl:hasBroadSynonym] lake
WARN duplicate_scoped_synonym bayou [ENVO:00000234] has_related_synonym [oboInOwl:hasRelatedSynonym] lake
WARN duplicate_scoped_synonym seamount [ENVO:00000264] has_broad_synonym [oboInOwl:hasBroadSynonym] mount
WARN duplicate_scoped_synonym seamount [ENVO:00000264] has_related_synonym [oboInOwl:hasRelatedSynonym] mount
WARN duplicate_scoped_synonym watershed [ENVO:00000292] has_exact_synonym [oboInOwl:hasExactSynonym] divide
WARN duplicate_scoped_synonym watershed [ENVO:00000292] has_related_synonym [oboInOwl:hasRelatedSynonym] divide
WARN duplicate_scoped_synonym ice cap dome [ENVO:00000342] has_exact_synonym [oboInOwl:hasExactSynonym] icecap dome
WARN duplicate_scoped_synonym ice cap dome [ENVO:00000342] has_narrow_synonym [oboInOwl:hasNarrowSynonym] icecap dome
WARN duplicate_scoped_synonym woodland clearing [ENVO:00000444] has_exact_synonym [oboInOwl:hasExactSynonym] clearing
WARN duplicate_scoped_synonym woodland clearing [ENVO:00000444] has_related_synonym [oboInOwl:hasRelatedSynonym] clearing
WARN duplicate_scoped_synonym container of an intermittent pond [ENVO:00000504] has_exact_synonym [oboInOwl:hasExactSynonym] intermittent pool
WARN duplicate_scoped_synonym container of an intermittent pond [ENVO:00000504] has_narrow_synonym [oboInOwl:hasNarrowSynonym] intermittent pool
WARN duplicate_scoped_synonym container of an intermittent pond [ENVO:00000504] has_related_synonym [oboInOwl:hasRelatedSynonym] intermittent pool
WARN duplicate_scoped_synonym terrace [ENVO:00000508] has_narrow_synonym [oboInOwl:hasNarrowSynonym] bench
WARN duplicate_scoped_synonym terrace [ENVO:00000508] has_related_synonym [oboInOwl:hasRelatedSynonym] bench
WARN duplicate_scoped_synonym lost stream [ENVO:00000517] has_broad_synonym [oboInOwl:hasBroadSynonym] lost river
WARN duplicate_scoped_synonym lost stream [ENVO:00000517] has_narrow_synonym [oboInOwl:hasNarrowSynonym] lost river
WARN duplicate_scoped_synonym ice cap depression [ENVO:00000531] has_exact_synonym [oboInOwl:hasExactSynonym] icecap depression
WARN duplicate_scoped_synonym ice cap depression [ENVO:00000531] has_related_synonym [oboInOwl:hasRelatedSynonym] icecap depression
WARN duplicate_scoped_synonym waterhole [ENVO:00000547] has_exact_synonym [oboInOwl:hasExactSynonym] water hole
WARN duplicate_scoped_synonym waterhole [ENVO:00000547] has_related_synonym [oboInOwl:hasRelatedSynonym] water hole
WARN duplicate_scoped_synonym glaze ice layer [ENVO:01000547] has_broad_synonym [oboInOwl:hasBroadSynonym] glaze
WARN duplicate_scoped_synonym glaze ice layer [ENVO:01000547] has_related_synonym [oboInOwl:hasRelatedSynonym] glaze

@kaiiam kaiiam added the thoughts things to continue thinking about label Aug 6, 2022
@pbuttigieg
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Closing as obsolete - but we should re-run this and chip away at the inconsistencies found here and in #1334

@pbuttigieg pbuttigieg closed this as not planned Won't fix, can't repro, duplicate, stale Aug 12, 2022
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