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ZFIN / zebrafish-anatomical-ontology

Ontology describing the anatomy of Danio rerio from a single cell to adult fish. The namespace of the ontology is zebrafish_anatomical_ontology the prefix is ZFA. Updates to ZFA are released every other month. A subset of the ZFS http://purl.obolibrary.org/obo/zfs.obo is packaged with this ontology.
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Syntax error in preversion #9

Closed cerivs closed 9 years ago

cerivs commented 10 years ago

red ball: http://build.berkeleybop.org/job/check-uberon-zfa/

holds_over_chain requires two arguments:

[Typedef]
id: RO:0002254
name: has developmental contribution from
def: "x has developmental contribution from y iff x has some part z such that z develops from y." [goc:cjm]
synonym: "has_developmental_contribution_from" EXACT []
xref: RO:0002254
***holds_over_chain: develops_from

The chain (in OWL) is

has_developmental_contribution_from <- has_part o develops_from

written in obo as:

holds_over_chain: has_part develops_from

I'm glad you're adding these, but copying and pasting relations in obo can be tricky. There are also methods to be able to use the symbolic form in relationship tags.

Feel free to call on me on the obo-anatomy list for help here.

Original comment by: cmungall

cerivs commented 10 years ago

I can send you a patch

Original comment by: cmungall

cerivs commented 10 years ago

Need patch because OE gives error Load Error, line -1 Assigned non-existant property in chain id has_part in term RO:0002254 org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1424) org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79)

if use "holds_over_chain: has_part develops_from" which is why I truncated

Original comment by: cerivs

cerivs commented 10 years ago

getting relations in place for NC work.

Original comment by: cerivs

cerivs commented 10 years ago

Need patch.

Original comment by: cerivs

cerivs commented 10 years ago

Original comment by: cmungall

cerivs commented 10 years ago

This has been fixed thanks

Original comment by: cmungall