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tair / toastdos-back

The back-end system for the GOAT community annotation tool
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conditional display of 'Evidence with' not working #312

Closed tberardini closed 5 years ago

tberardini commented 5 years ago

To reproduce: http://52.14.163.196:4200, login and go to submission

  1. PMID = 27095837
  2. Locus = AT5G37820
  3. Add a Biological process annotation for 'pollen germination'
  4. Select an evidence, 'double mutant phenotype evidence used in manual assertion'.
  5. No evidence with field shown.

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Compare with executing the same steps on toastdos.phoenixbioinformatics.org

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tberardini commented 5 years ago

related #185

JKingSE commented 5 years ago

The items we tested that we knew would need evidence now have it shown. However, as seen in the meeting, there was at least one class of items that needed evidence that didn't have it. That item was the item that started with "Double mutant". We will look into that one, but need this reviewed for any other possible missing areas.

lreiser commented 5 years ago

Per this discussion. Any selected method that maps to the code IGI or IPI should trigger the 'evidence with box'. mapping of ECO terms to GO evidence codes (e.g. IDA, IGI) here: http://purl.obolibrary.org/obo/eco/gaf-eco-mapping-derived.txt

Also the default 'relationship' type should be AND. The first addition would always be AND. OR would be used only when including more than one gene in Evidence with. I noticed the default display was OR. Should be like this.

evidencewith

lreiser commented 5 years ago

Here is the set of restrictions to display. This requires using the mapping file for ECO:GO (mapping ECO terms to the corresponding 3 letter evidence code which is in previously specified mapping file)

For each annotation (other than comment) the following restrictions apply Annotation Type: Evidence Type(s) Protein Interaction: IPI Molecular Function: IDA, IPI, IGI,IMP, EXP Cellular Component: IDA, IEP, EXP Biological Process:IDA, IMP, IGI, IPI, IEP, EXP Structure/Growth Development (expression annotations): IEP, IDA, EXP

lreiser commented 5 years ago

FWIW when testing other scenarios I used an IGI evidence method (suppressor/enhancer interaction phenotypic evidence used in manual assertion) and was properly and appropriately presented with the 'Evidence with' but using a different method (double mutant phenotypic evidence used in manual assertion) did not trigger the event. So it is inconsistent.

JKingSE commented 5 years ago

Using the reproduction steps above, this now appears. I'm not sure of exactly what other ways to get evidence with to appear, so this would need to be further tested by the sponsors.

JKingSE commented 5 years ago

'phage display evidence used in manual assertion' shows up one time 'double mutant phenotype evidence used in manual assertion' shows up three times with the same code, but different synonyms All other IGI codes are showing the evidence with section except for 'double mutant phenotype evidence used in manual assertion'.
The ecomap file does not include 'double mutant phenotype evidence used in manual assertion'. Evidence with shows up for eco codes matched to go codes.

tberardini commented 5 years ago

Opened ticket in ECO tracker: https://github.com/evidenceontology/evidenceontology/issues/216

lreiser commented 5 years ago

Confirmed that double mutant evidence code now works to trigger the evidence with field. screenshot_1656