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upa_nodes.tsv: All rows should have 14 columns #204

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hrshdhgd opened this issue Aug 4, 2024 · 2 comments
Open

upa_nodes.tsv: All rows should have 14 columns #204

hrshdhgd opened this issue Aug 4, 2024 · 2 comments
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@hrshdhgd
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hrshdhgd commented Aug 4, 2024

There are some rows that have just 8 columns and the 6 blank entries to make up the 14 columns are missing. So duckdb does not read them properly.

id category name description xref provided_by synonym iri object predicate relation same_as subject subsets
RHEA:19032
RHEA:20871
RHEA:32678
RHEA:10139
UPA:UCR00014 biolink:MolecularActivity pyruvate + thiamine diphosphate = 2-hydroxyethyl-ThPP + CO(2) upa.json http://purl.obolibrary.org/obo/UPa_UCR00014

The last line (and almost all like this) have no <tab>blank<tab> for the columns:

| object | predicate | relation | same_as | subject | subsets |

@hrshdhgd
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hrshdhgd commented Aug 4, 2024

Same goes for ec_nodes.tsv

@hrshdhgd
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hrshdhgd commented Aug 4, 2024

ec_edges.tsv also needs double checking. The columns are scrambled

subject predicate object relation primary_knowledge_source
urn:uuid:55d247c3-6b8f-4224-882e-6e19f81613b0 RO:0002327 biolink:inverseOf RO:0002333 inverseOf
urn:uuid:69e8fdb0-2c3c-4cfe-a2b4-bba96efa5e4d EC:1 biolink:subclass_of owl:Thing rdfs:subClassOf

First column is supposed to be id

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