Difference between revisions of "Annotation Conf. Call, July 28, 2015"

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(Overview by ontology editors)
(Example papers)
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===Example papers===
 
===Example papers===
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Obsoleted relationship:<br />
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localization_dependent_on<br />
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PMID: 22842922<br />
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DSF2 relocalizes from budneck to cytoplasm upon DNA replication stress<br>
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We would capture this as: cytoplasm, localization_dependent_on: GO:0006974 (cellular response to DNA damage stimulus) or<br>
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cytoplasm, in_presence_of: CHEBI: MMS/Hydroxyurea<br>
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(there are few papers in yeast where they have show localization changes in response to certain stimuli)
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Obsoleted relationship:<br>
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requires_substance<br />
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PMID: 11006294<br>
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ISC1 has inositol phosphosphingolipid phospholipase activity which is dependent on phosphatidylserine. We captured it with 'requires_substace' (in_presence_of would worked too). Both these relations are slated for obsoletion.
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Obsoleted relationship:<br />
 
Obsoleted relationship:<br />
 
independent_of <br />
 
independent_of <br />

Revision as of 12:27, 24 July 2015


Agenda

Overview by ontology editors

  • Nothing has been obsoleted, even if QuickGO webservice tests and their usage by Protein2GO have given that impression. The details of these tests and how they are used by protein2GO and GOA have [only just been documented](https://github.com/geneontology/annotation_extensions/wiki#checking-pipelines). We need to work with Tony S to provide a mechanism for suspending usage of potentially problematic relations pending review.
  • Annotation extension relationships are meant to extend the meaning of a GO term to create a new, more restricted class. Where the relation in question is used in GO, or is related logically to one that is, OWL translation of annotation extensions can be used to group annotations more accurately and potentially in useful novel ways (for example, grouping annotations to process term by the cell-type in which they occur). A small number of relations appear instead to qualify when the relationship between a GP and a GO term applies, (e.g. dependent_on, independent_of, in_presence_of, in_absence_of). OWL translation/interpretation of the resulting annotation extensions is problematic.

From reviewing usage of these relations, some are used with extremely variable semantics it seems there may be other more exotic uses (see review of [dependent_on usage](https://github.com/geneontology/annotation_extensions/issues/17).)

Given these issues, it is important to review usage of these relations to discuss what we are trying to achieve with respect to whether/how the annotations can be integrated into tools that support our users needs.


Example papers

Obsoleted relationship:
localization_dependent_on
PMID: 22842922
DSF2 relocalizes from budneck to cytoplasm upon DNA replication stress
We would capture this as: cytoplasm, localization_dependent_on: GO:0006974 (cellular response to DNA damage stimulus) or
cytoplasm, in_presence_of: CHEBI: MMS/Hydroxyurea
(there are few papers in yeast where they have show localization changes in response to certain stimuli)

Obsoleted relationship:
requires_substance
PMID: 11006294
ISC1 has inositol phosphosphingolipid phospholipase activity which is dependent on phosphatidylserine. We captured it with 'requires_substace' (in_presence_of would worked too). Both these relations are slated for obsoletion.

Obsoleted relationship:
independent_of
PMID:25215947
Typically mitophagy is dependent on PARK2 / parkin (Uniprot O60260). However, in PMID:25215947, authors show that AMBRA1 (Q9C0C7) (in presence of chemical inducers of mitochondrial depolarisation such as FCCP) initiates mitophagy independent of PARK2 / parkin. What to do now that independent_of relation is obsoleted? Simplest to create new term instead? e.g. “parkin-independent mitophagy in response to mitochondrial depolarization”.
NB Examples of parkin-independent mitophagy:
PMID: 25349190 "Parkin-independent mitophagy requires Drp1 and maintains the integrity of mammalian heart and brain."
PMID: 24176932 "Loss of iron triggers PINK1/Parkin-independent mitophagy."
Paul Denny, UCL Functional Annotation Group.

DOS: I'm happy to create a class for Parkin independent mitophagy

in_absence_of
Q75JZ1 gtaC
annotation: nucleus in_absence_of cAMP
PMID:24653039
Title of paper: Nucleocytoplasmic Shuttling of a GATA Transcription Factor Functions as a Development Timer. “We report here that GtaC exhibits rapid nucleocytoplasmic shuttling in response to periodic cAMP waves.” p1329
COMMENT: This was annotated in conjunction with a current ‘cytosol in_presence _of cAMP’ annotation. No other annotations would describe the shuttling as well as these two annotations together and in further conjunction with the annotation: regulation of aggregation involved in sorocarp development dependent_on cellular protein localization
NOTE: we already deleted this annotation as it was flagged in P2GO, but I really disliked deleting that one.

in_presence_of
Q550R2 ctxB
annotation: positive regulation of gene expression has_regulation_target carA, acaA, rasG,rasC, in_presence_of cAMP
PMID:22114350
FIGURE 6: Inhibition of cAMP-activation of Ras in ctxA−/B− cells. (A) cAMP activation of RasC and G.
FIGURE 5: Cortexillin-null cells have delayed and diminished expression of cAR1 and ACA. Suspensions of WT and cortexillin-null cells in starvation buffer were pulsed with cAMP…. ctxA− and ctxB− cells had delayed and reduced expression of ACA and cAR1, and ctxA−/B− cells had almost no expression of either ACA or cAR1.
COMMENT: Even though in Fig. 6 authors mention ‘cAMP activation, I like in_presence_of’ as it implies the correct thing; dependent_on implies that the regulation of the gene expression is dependent of cAMP, but it’s really dependent on the mutated gene(s) shown in this study. The addition of cAMP is mimicking natural starvation induced behaviour and in the assay they used cAMP. A more interpretive annotation would be:
positive regulation of gene expression has_regulation_target carA, acaA, rasG,rasC, happens_during response to starvation. Here the user must know what happens during starvation and it is more my interpretation than annotating what actually happens where users can interpret.

Q54BD4 dstC
annotation: response to cation stress happens_during sorocarp development in_presence_of potassium chloride
PMID: 22944283
There are four such annotations made for all 4 tested stress factors that resulted in developmental defects.
p.793: we investigated the development under stress of the dstC− (STATc) mutant. The dstC− mutant showed severe defects with fewer and/or smaller fruiting bodies under all of the stressing conditions (KCl, NaCl, MgCl2, LiCl) FIGURE 6. TacA is involved in the stress response during development.
COMMENT: Here it feels not appropriate to replace in_presence_of with ‘dependent_on’ and I would have lots of gripes against using ‘has_input’. Not clear what ‘has_agent’ means, never used that and wouldn’t like it either in this context.
Petra Fey, dictyBase