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taxon restriction for GO:0042633 hair cycle #11104

Closed gocentral closed 9 years ago

gocentral commented 10 years ago

GO:0042633 hair cycle has the rule "only_in_taxon 40674 Mammalia" but there is IEA from Ensembl Compara, so I would like to add the specific taxon restriction GO:0042633 hair cycle never_in_taxon 8782 Aves

GO:0048104 establishment of body hair or bristle planar orientation Should also have the rules – GO:0048104 establishment of body hair or bristle planar orientation only_in_taxon 40674 Mammalia GO:0048104 establishment of body hair or bristle planar orientation never_in_taxon 8782 Aves

Reported by: fmccarthy

Original Ticket: geneontology/ontology-requests/10920

gocentral commented 10 years ago

Original comment by: tberardini

gocentral commented 10 years ago

Added never in Aves for the two terms as requested but did not add:

GO:0048104 establishment of body hair or bristle planar orientation only_in_taxon 40674 Mammalia

The definition of that term refers to sensory bristles, which are found in Drosophila.

Original comment by: tberardini

gocentral commented 10 years ago

Errm, if you state only in Mammalia, then never_in_taxon Aves is not required.

Original comment by: cmungall

gocentral commented 10 years ago

That would seem to be true but from Fiona's comment ('but there is IEA from Ensembl Compara,'), something appears to be slipping through. Probably something more to do with Ensembl Compara than GO, since as you point out, adding never in Aves is not required. Was easy to add on a Friday afternoon though :). Fiona - you may want to follow up with the Compara folks (not sure who they are) about the pipeline.

Original comment by: tberardini

gocentral commented 10 years ago

I am trying to follow up with Compara. Last time I spoke to them they were making some fixes, so I kind of expected some fo these problems to go away

thanks!

On Mon, Jun 9, 2014 at 9:47 AM, Tanya Berardini tairtb@users.sf.net wrote:

That would seem to be true but from Fiona's comment ('but there is IEA from Ensembl Compara,'), something appears to be slipping through. Probably something more to do with Ensembl Compara than GO, since as you point out, adding never in Aves is not required. Was easy to add on a Friday afternoon though :). Fiona - you may want to follow up with the Compara folks (not sure who they are) about the pipeline.

Status: closed-fixed

Group: None Labels: Taxon restriction Created: Fri Jun 06, 2014 08:04 PM UTC by fmccarthy Last Updated: Sat Jun 07, 2014 05:17 PM UTC Owner: Tanya Berardini

GO:0042633 hair cycle has the rule "only_in_taxon 40674 Mammalia"

but there is IEA from Ensembl Compara, so I would like to add the specific taxon restriction GO:0042633 hair cycle never_in_taxon 8782 Aves

GO:0048104 establishment of body hair or bristle planar orientation Should also have the rules – GO:0048104 establishment of body hair or bristle planar orientation only_in_taxon 40674 Mammalia GO:0048104 establishment of body hair or bristle planar orientation

never_in_taxon 8782 Aves

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The AgBase Databases School of Animal and Comparative Biomedical Sciences & BIO5 University of Arizona Phone: 520-626-7321

http://www.agbase.msstate.edu/

Original comment by: fmccarthy

gocentral commented 10 years ago

Fiona, you told me that Ensembl are updating taxon constraints for the ver76 release. They released version 75 in February so they must be due another one pretty soon.

Rachael.

On 09/06/2014 19:37, Chris Mungall wrote:

OK - in general we won't be adding these redundant associations, so it's best if compara is fixed. Let us know if we can help

On 9 Jun 2014, at 10:22, fmccarthy wrote:

I am trying to follow up with Compara. Last time I spoke to them they were making some fixes, so I kind of expected some fo these problems to go away

  • but then I am not real clear on how they are applying the taxon rules to their Compara data.

thanks!

On Mon, Jun 9, 2014 at 9:47 AM, Tanya Berardini tairtb@users.sf.net wrote:

That would seem to be true but from Fiona's comment ('but there is IEA from Ensembl Compara,'), something appears to be slipping through. Probably something more to do with Ensembl Compara than GO, since as you point out, adding never in Aves is not required. Was easy to add on a Friday afternoon though :). Fiona - you may want to follow up with the Compara folks (not

sure who they are) about the pipeline.

Status: closed-fixed

Group: None Labels: Taxon restriction Created: Fri Jun 06, 2014 08:04 PM UTC by fmccarthy Last Updated: Sat Jun 07, 2014 05:17 PM UTC Owner: Tanya Berardini

GO:0042633 hair cycle has the rule "only_in_taxon 40674 Mammalia"

but there is IEA from Ensembl Compara, so I would like to add the specific taxon restriction GO:0042633 hair cycle never_in_taxon 8782 Aves

GO:0048104 establishment of body hair or bristle planar orientation Should also have the rules – GO:0048104 establishment of body hair or bristle planar orientation only_in_taxon 40674 Mammalia GO:0048104 establishment of body hair or bristle planar orientation

never_in_taxon 8782 Aves

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10920/

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The AgBase Databases School of Animal and Comparative Biomedical Sciences & BIO5 University of Arizona Phone: 520-626-7321

http://www.agbase.msstate.edu/

\ [ontology-requests:#10920] taxon restriction for GO:0042633 hair cycle**

Status: closed-fixed Group: None Labels: Taxon restriction Created: Fri Jun 06, 2014 08:04 PM UTC by fmccarthy Last Updated: Mon Jun 09, 2014 04:47 PM UTC Owner: Tanya Berardini

GO:0042633 hair cycle has the rule "only_in_taxon 40674
Mammalia" but there is IEA from Ensembl Compara, so I would like to add the specific taxon restriction GO:0042633 hair cycle never_in_taxon 8782 Aves

GO:0048104 establishment of body hair or bristle planar orientation Should also have the rules – GO:0048104 establishment of body hair or bristle planar orientation only_in_taxon 40674 Mammalia GO:0048104 establishment of body hair or bristle planar orientation never_in_taxon 8782 Aves

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Project Leader UniProt - Gene Ontology Annotation Project European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge, CB10 1SD United Kingdom

Email: huntley@ebi.ac.uk UniProt Gene Ontology Annotation Project: http://www.ebi.ac.uk/GOA http://twitter.com/emblebi

Original comment by: rachhuntley