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Knowledge-Graph-Hub / kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub
https://knowledge-graph-hub.github.io/kg-obo/getting_started.html
GNU General Public License v3.0
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`fobi` has duplicated prefixes #192

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

Describe the bug

Somewhere along the way, fobi nodes get assigned an incorrect CURIE prefix.

To Reproduce

$ wget https://kg-hub.berkeleybop.io/kg-obo/fobi/fobi/fobi_kgx_tsv.tar.gz
$ tar xvzf fobi_kgx_tsv.tar.gz
$ $ head fobi_kgx_tsv_nodes.tsv 
id      category        name    description     provided_by     iri     knowledge_source        object  predicate       relation        same_as    subject
FOODON:03411335 biolink:NamedThing      crab    Crabs are decapod crustaceans of the infraorder *Brachyura*, which typically have a very short projecting "tail", usually entirely hidden under the thorax. They live in all the world's oceans, in fresh water, and on land, are generally covered with a thick exoskeleton and have a single pair of claws. Many other animals with similar names - such as hermit crabs, king crabs, porcelain crabs, horseshoe crabs, and crab lice - are not true crabs.   Crabs are generally covered with a thick exoskeleton, composed primarily of highly mineralized chitin, and armed with a single pair of chelae (claws). Crabs are found in all of the world's oceans, while many crabs live in fresh water and on land, particularly in tropical regions. [https://en.wikipedia.org/wiki/Crab]  FOBI fobi       http://purl.obolibrary.org/obo/FOODON_03411335
CHEBI:16737     biolink:ChemicalSubstance       creatinine      A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. FOBI fobi       http://purl.obolibrary.org/obo/CHEBI_16737
FOBI.OWL#FOBI:050066    biolink:NamedThing      Avenanthramide Q                FOBI fobi       http://purl.obolibrary.org/obo/fobi.owl#FOBI_050066
FOBI.OWL#FOBI:050065    biolink:NamedThing      Avenanthramide P                FOBI fobi       http://purl.obolibrary.org/obo/fobi.owl#FOBI_050065
FOBI.OWL#FOBI:050064    biolink:NamedThing      Avenanthramide O                FOBI fobi       http://purl.obolibrary.org/obo/fobi.owl#FOBI_050064
FOBI.OWL#FOBI:050063    biolink:NamedThing      Avenanthramide C                FOBI fobi       http://purl.obolibrary.org/obo/fobi.owl#FOBI_050063
FOBI.OWL#FOBI:050062    biolink:NamedThing      Avenanthramide B                FOBI fobi       http://purl.obolibrary.org/obo/fobi.owl#FOBI_050062
FOBI.OWL#FOBI:050061    biolink:NamedThing      Avenanthramide A                FOBI fobi       http://purl.obolibrary.org/obo/fobi.owl#FOBI_050061
FOBI.OWL#FOBI:050060    biolink:NamedThing      2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one sulfate            FOBI fobi       http://purl.obolibrary.org/obo/fobi.owl#FOBI_050060

Expected behavior

The prefix should be FOBI:.

Version

f5be12cf1c0b52ad986568b5838a7a8f1cc36e5c