PAINT database update pipeline: Difference between revisions
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== | ==External info== | ||
https://docs.google.com/document/d/1Tx3DGLanQ1P6vBL6FWH5V5M7nVqCCCsqu-6m61jPtQ4/edit?usp=sharing | [https://docs.google.com/document/d/1Tx3DGLanQ1P6vBL6FWH5V5M7nVqCCCsqu-6m61jPtQ4/edit?usp=sharing Summary Google doc] | ||
[https://github.com/pantherdb/fullgo_paint_update fullgo_paint_update github repo] (This is the actual code that runs!) | |||
==Import EXP files== | ==Import EXP files== | ||
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* Managing differences: | * Managing differences: | ||
** Missing EXP evidence | ** Missing EXP evidence | ||
*** PAINT annotations are obsoleted if derived from GO EXP evidence is now missing. | |||
** New exp evidence | ** New exp evidence | ||
(see for ex https://github.com/pantherdb/fullgo_paint_update/issues/10) | *** Existing PAINT annotations are updated with new EXP evidence. | ||
*** Previously obsoleted PAINT annotations are "un-obsoleted" if new EXP evidence supporting it appears. | |||
; (see for ex https://github.com/pantherdb/fullgo_paint_update/issues/10) | |||
** Handling obsolete and merged terms | ** Handling obsolete and merged terms | ||
*** obsolete terms: | |||
a) has a 'replaced_by' tag | **** a) has a 'replaced_by' tag | ||
b) does not have a 'replaced_by' tag | ***** update GO and PAINT annotations to the new term and a message "[term] is obsoleted and replaced by [new term] so the annotation to [PTN####] is updated with new GO term" is outputted for PAINT annotations to this term. | ||
**** b) does not have a 'replaced_by' tag | |||
***** term and PAINT annotations are obsoleted and a message "[term] is obsoleted and no replaced term, so the annotation to [PTN####] is obsoleted" is outputted for PAINT annotations to this term | |||
** etc ? | ** etc ? | ||
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* List of messages for automatic changed: 'Comment' ('Update comment' in PAINT interface) | * List of messages for automatic changed: 'Comment' ('Update comment' in PAINT interface) | ||
** What types of messages ? obsoletes, missing EXP... what else ? | ** What types of messages ? obsoletes, missing EXP... what else ? | ||
** "[term] is obsoleted and replaced by [new term] so the annotation to [PTN####] is updated with new GO term" | |||
** "[term] is obsoleted and no replaced term, so the annotation to [PTN####] is obsoleted" | |||
* 'View omitted annotation information' -> generated on the fly ??? | * 'View omitted annotation information' -> generated on the fly ??? | ||
** What types of messages ? tree changes information (missing nodes) - what else ? | ** What types of messages ? tree changes information (missing nodes) - what else ? | ||
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[[Category: | |||
[[Category:PAINT]] |
Latest revision as of 09:47, 9 April 2019
External info
fullgo_paint_update github repo (This is the actual code that runs!)
Import EXP files
- File location:
http://geneontology.org/gene-associations/*.gaf.gz
Import ontology
- File location:
http://geneontology.org/ontology/go.obo
Integration with existing PAINT annotations
- Managing differences:
- Missing EXP evidence
- PAINT annotations are obsoleted if derived from GO EXP evidence is now missing.
- New exp evidence
- Existing PAINT annotations are updated with new EXP evidence.
- Previously obsoleted PAINT annotations are "un-obsoleted" if new EXP evidence supporting it appears.
- Missing EXP evidence
- Handling obsolete and merged terms
- obsolete terms:
- a) has a 'replaced_by' tag
- update GO and PAINT annotations to the new term and a message "[term] is obsoleted and replaced by [new term] so the annotation to [PTN####] is updated with new GO term" is outputted for PAINT annotations to this term.
- b) does not have a 'replaced_by' tag
- term and PAINT annotations are obsoleted and a message "[term] is obsoleted and no replaced term, so the annotation to [PTN####] is obsoleted" is outputted for PAINT annotations to this term
- a) has a 'replaced_by' tag
- obsolete terms:
- etc ?
- Handling obsolete and merged terms
- List of messages for automatic changed: 'Comment' ('Update comment' in PAINT interface)
- What types of messages ? obsoletes, missing EXP... what else ?
- "[term] is obsoleted and replaced by [new term] so the annotation to [PTN####] is updated with new GO term"
- "[term] is obsoleted and no replaced term, so the annotation to [PTN####] is obsoleted"
- 'View omitted annotation information' -> generated on the fly ???
- What types of messages ? tree changes information (missing nodes) - what else ?