#10920 taxon restriction for GO:0042633 hair cycle

[fmccarthy]

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

[Tanya Berardini]

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.

[Chris Mungall]

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

[Tanya Berardini]

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.

[fmccarthy]

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.

---

• [ontology-requests:#10920]
  http://sourceforge.net/p/geneontology/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: 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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Phone: 520-626-7321

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[rach_huntley]

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.

---

• [ontology-requests:#10920]
  http://sourceforge.net/p/geneontology/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: 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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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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https://sourceforge.net/p/geneontology/ontology-requests/10920/

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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
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