Annotation Conf. Call, June 23, 2015: Difference between revisions

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| GO:0097367  
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| ATP1A2
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| 1/4: (dependent_on GO:0031402 sodium ion binding, GO:0030955 potassium ion binding)
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| ATP binding
| GO:0005524
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| IDA-1, IMP-1
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| 1/4: (dependent_on GO:0031402 sodium ion binding, GO:0030955 potassium ion binding)
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| ATP1B1
| contributes_to
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| GO:0005524
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| 1/4: (dependent_on GO:0031402 sodium ion binding, GO:0030955 potassium ion binding)
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Revision as of 08:53, 23 June 2015


Agenda

Ability to add comments to an annotation

We want to be able to capture why a particular experiment/result was not captured as an annotation and make this comment visible to the public. This issue came up during the April curation consistency discussion (mouse paper). I made a github ticket. https://github.com/ebi-uniprot/Protein2GO/issues/1 How should we control this field so we don't write long sentences? Limit it to 140 characters? Other ideas?

obsolete relationships

There are some relationships that were obsoleted (mostly for use with col-16). Not sure how other groups are rehousing these annotations. Instead of a regular consistency exercise is it okay if we go through some of the papers and get your input on how to rehouse those col-16 data?

Note there are also 2 relationships which have been suggested to be obsoleted: dependent on in presence of

These pages list some of the use cases and try to suggest alternative ways to capture this data. A similar approach is required for the relationships that are now obsolete.

June Consistency paper

http://www.ncbi.nlm.nih.gov/pubmed/?term=23954377

Comments from groups re annotation

  • Ouabain plant derived drug used to treat hypotension and some arrhythmias, but also toxic.
  • We debated about annotating to sodium:potassium-exchanging ATPase activity - GO:0005391, but there is no exp. evidence to show that there was indeed exchange of these ions. There is no data for the term ATPase, coupled either. Without using background knowledge we cannot make the granular annotation based on just this paper.
  • The authors express ATP1A2 and ATP1B1. But there is not enough data in this paper to say that alpha and beta subunits contribute to the activity. So we did not capture annotations to beta subunit.
  • Normally we won't make the annotations to potassium ion binding and sodium ion binding, but if this is the only paper on this protein these annotations are acceptable
  • There is no background measurement for activity without the transfected proteins (negative control) - although there are measurements for activity of mutants which have lower activity.

Annotation Summary

Gene Qualifier Term ID # of Annotations Evidence Code Summary 'With' field Summary Extension Summary
Molecular Function Annotations
ATP1A2 contributes_to drug binding GO:0008144 1/4 IPI CHEBI:472805 - ouabain
ATP1B1 contributes_to drug binding GO:0008144 1/4 IPI CHEBI:472805 - ouabain
ATP1A2 contributes_to carbohydrate derivative binding GO:0097367 1/4 IPI CHEBI:472805 - ouabain
ATP1B1 contributes_to carbohydrate derivative binding GO:0097367 1/4 IPI CHEBI:472805 - ouabain
ATP1A2 contributes_to sodium ion binding GO:0097367 2/4 IDA-1, IMP-1
ATP1A2 sodium ion binding GO:0097367 1/4 IDA, IMP (in_presence_of CHEBI:29103 Potassium AND P05026 ATP1B1)
ATP1B1 contributes_to sodium ion binding GO:0097367 2/4 IDA
ATP1A2 contributes_to potassium ion binding GO:0030955 2/4 IDA-1, IMP-1
ATP1A2 potassium ion binding GO:0030955 1/4 IDA, IMP (in_presence_of CHEBI:29101 Sodium AND P05026 ATP1B1)
ATP1B1 contributes_to potassium ion binding GO:0030955 2/4 IDA
ATP1A2 contributes_to ATPase activity GO:0016887 2/4 IDA-1, IMP-1 1/4: (dependent_on GO:0031402 sodium ion binding, GO:0030955 potassium ion binding)
ATP1A2 ATPase activity GO:0016887 1/4 IDA, IMP (in_presence_of CHEBI:29101 Sodium AND CHEBI:29103 Potassium AND UniProt: P05026 ATP1B1)
ATP1B1 contributes_to ATPase activity GO:0016887 2/4 IDA 1/4: (dependent_on GO:0031402 sodium ion binding, GO:0030955 potassium ion binding)
ATP1A2 contributes_to ATP binding GO:0005524 2/4 IDA-1, IMP-1 1/4: (dependent_on GO:0031402 sodium ion binding, GO:0030955 potassium ion binding)
ATP1B1 contributes_to ATP binding GO:0005524 2/4 IDA 1/4: (dependent_on GO:0031402 sodium ion binding, GO:0030955 potassium ion binding)
ATP1A2 ATPase binding GO:0051117 1/4 IPI ATP1B1
ATP1B1 ATPase binding GO:0051117 1/4 IPI ATP1A2
ATP1A2 contributes_to sodium:potassium-exchanging ATPase activity GO:0005391 1/4 IDA/IMP
ATP1A2 contributes_to sodium:potassium-exchanging ATPase activity GO:0005391 1/4 IC GO:0031402 sodium ion binding, GO:0030955 potassium ion binding, GO:0016887 ATPase activity, GO:0016020 membrane
ATP1B1 contributes_to sodium:potassium-exchanging ATPase activity GO:0005391 1/4 IDA/IMP
ATP1B1 contributes_to sodium:potassium-exchanging ATPase activity GO:0005391 1/4 IC GO:0031402 sodium ion binding, GO:0030955 potassium ion binding, GO:0016887 ATPase activity, GO:0016020 membrane
Biological Process Annotations
ATP1A2 potassium ion import across plasma membrane GO:1990573 1/3 IC GO:0030955 potassium ion binding, GO:0016887 ATPase activity, GO:0016020 membrane
ATP1A2 cellular potassium ion homeostasis GO:0030007 1/3 IC GO:0030955 potassium ion binding, GO:0016887 ATPase activity, GO:0016020 membrane
ATP1A2 regulation of synaptic transmission, glutamatergic GO:0051966 1/3 NAS
ATP1A2 regulation of glutamate uptake involved in transmission of nerve impulse GO:0051946 1/3 NAS
ATP1A2 membrane repolarization GO:0086009 1/3 TAS (occurs_in UBERON_0000955, brain)
Cellular Component Annotations
ATP1A2 membrane GO:0016020 3/3 IDA
ATP1B1 membrane GO:0016020 3/3 IDA
ATP1A2 sodium:potassium-exchanging ATPase complex GO:0005890 1/3 IDA
ATP1B1 sodium:potassium-exchanging ATPase complex GO:0005890 1/3 IDA