🍓 Update oquat

biopragmatics · May 21, 2023 · a6e6e93 · a6e6e93
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diff --git a/docs/failures.md b/docs/failures.md
diff --git a/docs/invalids/README.md b/docs/invalids/README.md
diff --git a/docs/invalids/prefix/aao.md b/docs/invalids/prefix/aao.md
@@ -2,9 +2,40 @@
 
 This page summarize the different resources that reference `aao`
 but use local unique identifiers that do not match the standard pattern of
-`^\d{7}$`. Of the 1 resources,
+`^\d{7}$`. Of the 2 resources,
 1 variants on the standard prefix were found: ['AAO'].
 
+## `nif`: None
+
+Identifiers for this prefix are given incorrectly in `nif`.
+
+| external_xref                 |   usages_count | usages                                                                                                                                                                                                                                                                                                                                   |
+|-------------------------------|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `AAO:LAP`                     |            251 | [UBERON:0001080](http://purl.obolibrary.org/obo/UBERON_0001080), [UBERON:0002375](http://purl.obolibrary.org/obo/UBERON_0002375), [UBERON:0012129](http://purl.obolibrary.org/obo/UBERON_0012129), [UBERON:0014898](http://purl.obolibrary.org/obo/UBERON_0014898), [UBERON:0034900](http://purl.obolibrary.org/obo/UBERON_0034900), ... |
+| `AAO:EJS`                     |            116 | [UBERON:0013732](http://purl.obolibrary.org/obo/UBERON_0013732), [UBERON:3000237](http://purl.obolibrary.org/obo/UBERON_3000237), [UBERON:3000265](http://purl.obolibrary.org/obo/UBERON_3000265), [UBERON:3000288](http://purl.obolibrary.org/obo/UBERON_3000288), [UBERON:3000323](http://purl.obolibrary.org/obo/UBERON_3000323), ... |
+| `AAO:BJB`                     |             59 | [UBERON:3000041](http://purl.obolibrary.org/obo/UBERON_3000041), [UBERON:3000044](http://purl.obolibrary.org/obo/UBERON_3000044), [UBERON:3010029](http://purl.obolibrary.org/obo/UBERON_3010029), [UBERON:3010039](http://purl.obolibrary.org/obo/UBERON_3010039), [UBERON:3010042](http://purl.obolibrary.org/obo/UBERON_3010042), ... |
+| `AAO:BMZ`                     |             30 | [UBERON:3010586](http://purl.obolibrary.org/obo/UBERON_3010586), [UBERON:3010589](http://purl.obolibrary.org/obo/UBERON_3010589), [UBERON:3010590](http://purl.obolibrary.org/obo/UBERON_3010590), [UBERON:3010613](http://purl.obolibrary.org/obo/UBERON_3010613), [UBERON:3010614](http://purl.obolibrary.org/obo/UBERON_3010614), ... |
+| `AAO:MEJ`                     |             17 | [UBERON:3010673](http://purl.obolibrary.org/obo/UBERON_3010673), [UBERON:3010691](http://purl.obolibrary.org/obo/UBERON_3010691), [UBERON:3010692](http://purl.obolibrary.org/obo/UBERON_3010692), [UBERON:3010694](http://purl.obolibrary.org/obo/UBERON_3010694), [UBERON:3010695](http://purl.obolibrary.org/obo/UBERON_3010695), ... |
+| `AAO:Trueb_1973`              |              8 | [UBERON:3000711](http://purl.obolibrary.org/obo/UBERON_3000711), [UBERON:3000712](http://purl.obolibrary.org/obo/UBERON_3000712), [UBERON:3000717](http://purl.obolibrary.org/obo/UBERON_3000717), [UBERON:3000793](http://purl.obolibrary.org/obo/UBERON_3000793), [UBERON:3000794](http://purl.obolibrary.org/obo/UBERON_3000794), ... |
+| `AAO:SIQ`                     |              8 | [UBERON:3010105](http://purl.obolibrary.org/obo/UBERON_3010105), [UBERON:3010765](http://purl.obolibrary.org/obo/UBERON_3010765), [UBERON:3010778](http://purl.obolibrary.org/obo/UBERON_3010778), [UBERON:3010796](http://purl.obolibrary.org/obo/UBERON_3010796), [UBERON:3010798](http://purl.obolibrary.org/obo/UBERON_3010798), ... |
+| `AAO:Francis_1934`            |              6 | [UBERON:3000694](http://purl.obolibrary.org/obo/UBERON_3000694), [UBERON:3000950](http://purl.obolibrary.org/obo/UBERON_3000950), [UBERON:3000951](http://purl.obolibrary.org/obo/UBERON_3000951), [UBERON:3000952](http://purl.obolibrary.org/obo/UBERON_3000952), [UBERON:3000954](http://purl.obolibrary.org/obo/UBERON_3000954), ... |
+| `AAO:Pugener_2002`            |              5 | [UBERON:3000711](http://purl.obolibrary.org/obo/UBERON_3000711), [UBERON:3000712](http://purl.obolibrary.org/obo/UBERON_3000712), [UBERON:3000717](http://purl.obolibrary.org/obo/UBERON_3000717), [UBERON:3000727](http://purl.obolibrary.org/obo/UBERON_3000727), [UBERON:3000735](http://purl.obolibrary.org/obo/UBERON_3000735)      |
+| `AAO:Maglia_et_al_2007`       |              4 | [UBERON:0006714](http://purl.obolibrary.org/obo/UBERON_0006714), [UBERON:0006715](http://purl.obolibrary.org/obo/UBERON_0006715), [UBERON:3000746](http://purl.obolibrary.org/obo/UBERON_3000746), [UBERON:3000810](http://purl.obolibrary.org/obo/UBERON_3000810)                                                                       |
+| `AAO:CAM`                     |              4 | [UBERON:3010720](http://purl.obolibrary.org/obo/UBERON_3010720), [UBERON:3010722](http://purl.obolibrary.org/obo/UBERON_3010722), [UBERON:3010751](http://purl.obolibrary.org/obo/UBERON_3010751), [UBERON:3010764](http://purl.obolibrary.org/obo/UBERON_3010764)                                                                       |
+| `AAO:Pugener_and_Maglia_2008` |              3 | [UBERON:0001079](http://purl.obolibrary.org/obo/UBERON_0001079), [UBERON:0006062](http://purl.obolibrary.org/obo/UBERON_0006062), [UBERON:3000745](http://purl.obolibrary.org/obo/UBERON_3000745)                                                                                                                                        |
+| `AAO:Duellman_and_Trueb_1994` |              3 | [UBERON:3000707](http://purl.obolibrary.org/obo/UBERON_3000707), [UBERON:3000728](http://purl.obolibrary.org/obo/UBERON_3000728), [UBERON:3000956](http://purl.obolibrary.org/obo/UBERON_3000956)                                                                                                                                        |
+| `AAO:Griffiths_1959`          |              3 | [UBERON:3000718](http://purl.obolibrary.org/obo/UBERON_3000718), [UBERON:3000719](http://purl.obolibrary.org/obo/UBERON_3000719), [UBERON:3000720](http://purl.obolibrary.org/obo/UBERON_3000720)                                                                                                                                        |
+| `AAO:DSM`                     |              2 | [UBERON:0009121](http://purl.obolibrary.org/obo/UBERON_0009121), [UBERON:3010632](http://purl.obolibrary.org/obo/UBERON_3010632)                                                                                                                                                                                                         |
+| `AAO:LT`                      |              2 | [UBERON:3000074](http://purl.obolibrary.org/obo/UBERON_3000074), [UBERON:3010576](http://purl.obolibrary.org/obo/UBERON_3010576)                                                                                                                                                                                                         |
+| `AAO:curator`                 |              2 | [UBERON:3000588](http://purl.obolibrary.org/obo/UBERON_3000588), [UBERON:3010138](http://purl.obolibrary.org/obo/UBERON_3010138)                                                                                                                                                                                                         |
+| `AAO:Rocek_2003`              |              2 | [UBERON:3000683](http://purl.obolibrary.org/obo/UBERON_3000683), [UBERON:3000685](http://purl.obolibrary.org/obo/UBERON_3000685)                                                                                                                                                                                                         |
+| `AAO:Kluge_and_Farris_1969`   |              2 | [UBERON:3000713](http://purl.obolibrary.org/obo/UBERON_3000713), [UBERON:3000714](http://purl.obolibrary.org/obo/UBERON_3000714)                                                                                                                                                                                                         |
+| `AAO:Cannatella_1985`         |              2 | [UBERON:3000808](http://purl.obolibrary.org/obo/UBERON_3000808), [UBERON:3000809](http://purl.obolibrary.org/obo/UBERON_3000809)                                                                                                                                                                                                         |
+| `AAO:DBW`                     |              2 | [UBERON:3010583](http://purl.obolibrary.org/obo/UBERON_3010583), [UBERON:3010728](http://purl.obolibrary.org/obo/UBERON_3010728)                                                                                                                                                                                                         |
+| `AAO:JMG`                     |              2 | [UBERON:3010818](http://purl.obolibrary.org/obo/UBERON_3010818), [UBERON:3010819](http://purl.obolibrary.org/obo/UBERON_3010819)                                                                                                                                                                                                         |
+| `AAO:HM`                      |              1 | [UBERON:3010690](http://purl.obolibrary.org/obo/UBERON_3010690)                                                                                                                                                                                                                                                                          |
+| `AAO:AMM`                     |              1 | [UBERON:3010821](http://purl.obolibrary.org/obo/UBERON_3010821)                                                                                                                                                                                                                                                                          |
+
 ## `uberon`: Uber Anatomy Ontology
 
 Identifiers for this prefix are given incorrectly in `uberon`. See the [GitHub repository](https://github.com/obophenotype/uberon).

diff --git a/docs/invalids/prefix/aeo.md b/docs/invalids/prefix/aeo.md
@@ -2,7 +2,7 @@
 
 This page summarize the different resources that reference `aeo`
 but use local unique identifiers that do not match the standard pattern of
-`^\d{7}$`. Of the 2 resources,
+`^\d{7}$`. Of the 3 resources,
 2 variants on the standard prefix were found: ['AEO', 'AEO.'].
 
 ## `aeo`: Anatomical Entity Ontology
@@ -14,6 +14,15 @@ Identifiers for this prefix are given incorrectly in `aeo`. See the [GitHub repo
 | `AEO:JB`        |            111 | [AEO:0000078](http://purl.obolibrary.org/obo/AEO_0000078), [AEO:0000079](http://purl.obolibrary.org/obo/AEO_0000079), [AEO:0000080](http://purl.obolibrary.org/obo/AEO_0000080), [AEO:0000081](http://purl.obolibrary.org/obo/AEO_0000081), [AEO:0000082](http://purl.obolibrary.org/obo/AEO_0000082), ... |
 | `AEO.:JB`       |              1 | [AEO:0000203](http://purl.obolibrary.org/obo/AEO_0000203)                                                                                                                                                                                                                                                  |
 
+## `nif`: None
+
+Identifiers for this prefix are given incorrectly in `nif`.
+
+| external_xref   |   usages_count | usages                                                                                                                                                                                                                                                                                                                                   |
+|-----------------|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `AEO:JB`        |             30 | [UBERON:0001637](http://purl.obolibrary.org/obo/UBERON_0001637), [UBERON:0004016](http://purl.obolibrary.org/obo/UBERON_0004016), [UBERON:0005866](http://purl.obolibrary.org/obo/UBERON_0005866), [UBERON:0006846](http://purl.obolibrary.org/obo/UBERON_0006846), [UBERON:0007473](http://purl.obolibrary.org/obo/UBERON_0007473), ... |
+| `AEO:000020`    |              1 | [UBERON:0001013](http://purl.obolibrary.org/obo/UBERON_0001013)                                                                                                                                                                                                                                                                          |
+
 ## `uberon`: Uber Anatomy Ontology
 
 Identifiers for this prefix are given incorrectly in `uberon`. See the [GitHub repository](https://github.com/obophenotype/uberon).

diff --git a/docs/invalids/prefix/agricola.md b/docs/invalids/prefix/agricola.md
@@ -2,7 +2,7 @@
 
 This page summarize the different resources that reference `agricola`
 but use local unique identifiers that do not match the standard pattern of
-`^\d+$`. Of the 3 resources,
+`^\d+$`. Of the 4 resources,
 2 variants on the standard prefix were found: ['AGR', 'Agricola'].
 
 ## `chebi`: Chemical Entities of Biological Interest
@@ -505,6 +505,7 @@ Identifiers for this prefix are given incorrectly in `chebi`. See the [GitHub re
 | `AGR:IND43643995`  |              1 | [CHEBI:1945](http://purl.obolibrary.org/obo/CHEBI_1945)                                                                                                                           |
 | `AGR:IND43824488`  |              1 | [CHEBI:1945](http://purl.obolibrary.org/obo/CHEBI_1945)                                                                                                                           |
 | `AGR:IND601139292` |              1 | [CHEBI:1945](http://purl.obolibrary.org/obo/CHEBI_1945)                                                                                                                           |
+| `AGR:IND20609475`  |              1 | [CHEBI:194509](http://purl.obolibrary.org/obo/CHEBI_194509)                                                                                                                       |
 | `AGR:IND79007669`  |              1 | [CHEBI:20833](http://purl.obolibrary.org/obo/CHEBI_20833)                                                                                                                         |
 | `AGR:IND82043546`  |              1 | [CHEBI:20833](http://purl.obolibrary.org/obo/CHEBI_20833)                                                                                                                         |
 | `AGR:IND606859743` |              1 | [CHEBI:21347](http://purl.obolibrary.org/obo/CHEBI_21347)                                                                                                                         |
@@ -1151,7 +1152,7 @@ Identifiers for this prefix are given incorrectly in `chebi`. See the [GitHub re
 | `AGR:IND93043841`  |              1 | [CHEBI:9700](http://purl.obolibrary.org/obo/CHEBI_9700)                                                                                                                           |
 | `AGR:IND92029567`  |              1 | [CHEBI:9947](http://purl.obolibrary.org/obo/CHEBI_9947)                                                                                                                           |
 
-## `enm`: eNanoMapper Ontology
+## `enm`: eNanoMapper ontology
 
 Identifiers for this prefix are given incorrectly in `enm`.
 
@@ -1164,6 +1165,27 @@ Identifiers for this prefix are given incorrectly in `enm`.
 | `AGR:IND92003154` |              1 | [CHEBI:136644](http://purl.obolibrary.org/obo/CHEBI_136644) |
 | `AGR:IND43789627` |              1 | [CHEBI:136646](http://purl.obolibrary.org/obo/CHEBI_136646) |
 
+## `nif`: None
+
+Identifiers for this prefix are given incorrectly in `nif`.
+
+| external_xref      |   usages_count | usages                                                      |
+|--------------------|----------------|-------------------------------------------------------------|
+| `AGR:IND84086009`  |              1 | [CHEBI:136643](http://purl.obolibrary.org/obo/CHEBI_136643) |
+| `AGR:IND20386178`  |              1 | [CHEBI:136644](http://purl.obolibrary.org/obo/CHEBI_136644) |
+| `AGR:IND84086011`  |              1 | [CHEBI:136644](http://purl.obolibrary.org/obo/CHEBI_136644) |
+| `AGR:IND89021681`  |              1 | [CHEBI:136644](http://purl.obolibrary.org/obo/CHEBI_136644) |
+| `AGR:IND92003154`  |              1 | [CHEBI:136644](http://purl.obolibrary.org/obo/CHEBI_136644) |
+| `AGR:IND81078502`  |              1 | [CHEBI:15955](http://purl.obolibrary.org/obo/CHEBI_15955)   |
+| `AGR:IND605478333` |              1 | [CHEBI:16522](http://purl.obolibrary.org/obo/CHEBI_16522)   |
+| `AGR:IND607198670` |              1 | [CHEBI:16709](http://purl.obolibrary.org/obo/CHEBI_16709)   |
+| `AGR:IND606960789` |              1 | [CHEBI:27470](http://purl.obolibrary.org/obo/CHEBI_27470)   |
+| `AGR:IND605848433` |              1 | [CHEBI:28934](http://purl.obolibrary.org/obo/CHEBI_28934)   |
+| `AGR:IND607339542` |              1 | [CHEBI:3312](http://purl.obolibrary.org/obo/CHEBI_3312)     |
+| `AGR:IND43941110`  |              1 | [CHEBI:62546](http://purl.obolibrary.org/obo/CHEBI_62546)   |
+| `AGR:IND44688035`  |              1 | [CHEBI:87230](http://purl.obolibrary.org/obo/CHEBI_87230)   |
+| `AGR:IND607175662` |              1 | [CHEBI:9506](http://purl.obolibrary.org/obo/CHEBI_9506)     |
+
 ## `po`: Plant Ontology
 
 Identifiers for this prefix are given incorrectly in `po`. See the [GitHub repository](https://github.com/Planteome/plant-ontology).

diff --git a/docs/invalids/prefix/biorxiv.md b/docs/invalids/prefix/biorxiv.md
@@ -2,9 +2,17 @@
 
 This page summarize the different resources that reference `biorxiv`
 but use local unique identifiers that do not match the standard pattern of
-`^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$`. Of the 1 resources,
+`^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$`. Of the 2 resources,
 1 variants on the standard prefix were found: ['BioRXiv'].
 
+## `nif`: None
+
+Identifiers for this prefix are given incorrectly in `nif`.
+
+| external_xref                            |   usages_count | usages                                                  |
+|------------------------------------------|----------------|---------------------------------------------------------|
+| `BioRXiv:https://doi.org/10.1101/584664` |              1 | [SO:0002223](http://purl.obolibrary.org/obo/SO_0002223) |
+
 ## `so`: Sequence types and features ontology
 
 Identifiers for this prefix are given incorrectly in `so`. See the [GitHub repository](https://github.com/The-Sequence-Ontology/SO-Ontologies).

diff --git a/docs/invalids/prefix/birnlex.md b/docs/invalids/prefix/birnlex.md
@@ -2,9 +2,18 @@
 
 This page summarize the different resources that reference `birnlex`
 but use local unique identifiers that do not match the standard pattern of
-`^\d+$`. Of the 1 resources,
+`^\d+$`. Of the 2 resources,
 1 variants on the standard prefix were found: ['BIRNLEX'].
 
+## `nif`: None
+
+Identifiers for this prefix are given incorrectly in `nif`.
+
+| external_xref           |   usages_count | usages                                                          |
+|-------------------------|----------------|-----------------------------------------------------------------|
+| `BIRNLEX:Limbic_system` |              1 | [UBERON:0000349](http://purl.obolibrary.org/obo/UBERON_0000349) |
+| `BIRNLEX:4106_2`        |              1 | [UBERON:0000396](http://purl.obolibrary.org/obo/UBERON_0000396) |
+
 ## `uberon`: Uber Anatomy Ontology
 
 Identifiers for this prefix are given incorrectly in `uberon`. See the [GitHub repository](https://github.com/obophenotype/uberon).