QCQA call 2018-03-20: Difference between revisions
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What do we want to report on? | What do we want to report on? | ||
Review Cambridge meeting minutes: https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit | Review Cambridge meeting minutes: https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit | ||
* HTP report (Helen) | |||
* HTP/ propagation: do we have guidelines yet? | |||
* Annotation reviews: update; perspective | |||
* How GO annotation errors can affect analysis: https://github.com/geneontology/go-annotation/issues/1869 | |||
* Berkeley should provide a report for each organism for a slim to see if there are major (unexpected) changes | |||
* Priorities for annotation reviews: could be driven by the slim analysis: when numbers seem inconsistent (between IBA+IEAInterPro) AND EXP, especially when the numbers are high | |||
* Major causes of errors/ inconsistencies/ omissions (see below) | |||
* Derivative annotations must be flagged/and filtered (done automatically in P2GO - this need to be done at GOC as well) | |||
* Improve guidelines: again, prioritize which guidelines to update; get each group to review the new guidelines | |||
==General overview== | |||
====How GO annotation errors/ inconsistencies/ ommissions can affect analysis==== | ====How GO annotation errors/ inconsistencies/ ommissions can affect analysis==== | ||
https://github.com/geneontology/go-annotation/issues/1869 | |||
* Encourage people to think about annotation depth (cytoplasmic translation) | * Encourage people to think about annotation depth ( e.g. cytoplasmic translation) | ||
* Slim numbers *should* now be relatively stable now (ontology wise), and only affected by annotation increases and decreases ( I might be able to illustrate how errors affect analyses...) | * Slim numbers *should* now be relatively stable now (ontology wise), and only affected by annotation increases and decreases ( I might be able to illustrate how errors affect analyses...) | ||
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: i) Blocking of very general high-level GO terms to increase specificity | : i) Blocking of very general high-level GO terms to increase specificity | ||
:: https://github.com/geneontology/go-annotation/issues/1659 | |||
: ii) Taxon constraints (broken?) | : ii) Taxon constraints (broken?) | ||
: iii) Other rules? | : iii) Other rules? (Matrix see below) | ||
* Annotation reviews from ontology development work | * Annotation reviews from ontology development work | ||
: examples | : examples | ||
: identifies | : identifies: | ||
:: Specificity in the ontology changed to annotation+ extension | :: Specificity in the ontology changed to annotation+ extension | ||
:: general curator error | :: general curator error | ||
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: https://drive.google.com/drive/folders/0B0YtE_BqXTzQbkdFZmwzV1M2TjA | : https://drive.google.com/drive/folders/0B0YtE_BqXTzQbkdFZmwzV1M2TjA | ||
:identifies | : identifies: | ||
:: general curation errors | :: general curation errors | ||
:: ontology fixes (true path violations and missing parent) | :: ontology fixes (true path violations and missing parent) | ||
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* other methods | * other methods | ||
====Summarize major causes of errors/ inconsistencies/ omissions==== | |||
* a) experimental readout | |||
a) experimental readout | * b) annotating a cargo or target to a process | ||
b) annotating a cargo or target to a process | * c) ignoring author intent | ||
c) ignoring author intent | * d) New biological insights | ||
d) New biological insights https://github.com/geneontology/go-annotation/issues/1806 | : https://github.com/geneontology/go-annotation/issues/1806 | ||
e) A phenotype not specific for a process | : we need a list of blacklisted papers and retractions | ||
* e) A phenotype not specific for a process | |||
etc | etc | ||
Why we should prioritise error fixing | ====Why we should prioritise error fixing==== | ||
* Should be considered critical like fixing bugs in software | |||
* Small errors can uncover large issues (fix many problems simultaneously across multiple species) | |||
* Prevents future propagation, via PAINt, Ensembl, InterPro mappings | |||
What next? | ====What next?==== | ||
* Removing redundancy? | * Removing redundancy? this is related to QC. When the redundancy is removed its easier to spot errors | ||
https://github.com/geneontology/go-annotation/issues/1544 | : https://github.com/geneontology/go-site/issues/436 | ||
https://github.com/geneontology/go-annotation/issues/1674 | : https://github.com/geneontology/go-annotation/issues/1544 | ||
https://github.com/geneontology/amigo/issues/43 | : https://github.com/geneontology/go-annotation/issues/1674 | ||
https://github.com/geneontology/amigo/issues/295 | : https://github.com/geneontology/amigo/issues/43 | ||
https://github.com/geneontology/amigo/issues/440 | : https://github.com/geneontology/amigo/issues/295 | ||
: https://github.com/geneontology/amigo/issues/440 | |||
* Really need a way to identify unsupported ISS annotation (there is no alerting when the primary annotation is removed) | * Really need a way to identify unsupported ISS annotation (there is no alerting when the primary annotation is removed) | ||
* | * Block terms not suitable for annotation transfer | ||
examples | examples | ||
transporter specificity (changes frequently between species) | transporter specificity (changes frequently between species) | ||
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response to terms | response to terms | ||
add examples.... | add examples.... | ||
* I would like to propose that we phase out TAS and NAS (not used for future annotations). Should always be an experiment (or an ISO is better than TAS/NAS) | |||
==Rules for protein complexes in 'with' column== | ==Rules for protein complexes in 'with' column== | ||
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[[Category:Quality Control | ==Meeting notes== | ||
* Ask PIs/managers: every contributing group should have one member attending annotation call | |||
* Contributing groups that do not participate must give access to their annotations OR we reserve the right to filter out annotations that do not match our criteria | |||
* Many RCA annotations come from AgBase and Gramene, who haven't responded to our requests | |||
[[Category:Quality Control]] |
Latest revision as of 09:54, 15 April 2019
Agenda
GOC NYC May 2018
What do we want to report on? Review Cambridge meeting minutes: https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit
- HTP report (Helen)
- HTP/ propagation: do we have guidelines yet?
- Annotation reviews: update; perspective
- How GO annotation errors can affect analysis: https://github.com/geneontology/go-annotation/issues/1869
- Berkeley should provide a report for each organism for a slim to see if there are major (unexpected) changes
- Priorities for annotation reviews: could be driven by the slim analysis: when numbers seem inconsistent (between IBA+IEAInterPro) AND EXP, especially when the numbers are high
- Major causes of errors/ inconsistencies/ omissions (see below)
- Derivative annotations must be flagged/and filtered (done automatically in P2GO - this need to be done at GOC as well)
- Improve guidelines: again, prioritize which guidelines to update; get each group to review the new guidelines
General overview
How GO annotation errors/ inconsistencies/ ommissions can affect analysis
https://github.com/geneontology/go-annotation/issues/1869
- Encourage people to think about annotation depth ( e.g. cytoplasmic translation)
- Slim numbers *should* now be relatively stable now (ontology wise), and only affected by annotation increases and decreases ( I might be able to illustrate how errors affect analyses...)
How errors /inconsistencies/ ommissions are identified
- Rules
- i) Blocking of very general high-level GO terms to increase specificity
- ii) Taxon constraints (broken?)
- iii) Other rules? (Matrix see below)
- Annotation reviews from ontology development work
- examples
- identifies:
- Specificity in the ontology changed to annotation+ extension
- general curator error
- Matrix and slimming (assessing annotation at the organism level)
- https://www.slideshare.net/ValerieWood/copy-of-biocuration-2017
- https://drive.google.com/drive/folders/0B0YtE_BqXTzQbkdFZmwzV1M2TjA
- identifies:
- general curation errors
- ontology fixes (true path violations and missing parent)
- Incorrect IEA mappings (SPKW and InterPro)
- other methods
Summarize major causes of errors/ inconsistencies/ omissions
- a) experimental readout
- b) annotating a cargo or target to a process
- c) ignoring author intent
- d) New biological insights
- https://github.com/geneontology/go-annotation/issues/1806
- we need a list of blacklisted papers and retractions
- e) A phenotype not specific for a process
etc
Why we should prioritise error fixing
- Should be considered critical like fixing bugs in software
- Small errors can uncover large issues (fix many problems simultaneously across multiple species)
- Prevents future propagation, via PAINt, Ensembl, InterPro mappings
What next?
- Removing redundancy? this is related to QC. When the redundancy is removed its easier to spot errors
- https://github.com/geneontology/go-site/issues/436
- https://github.com/geneontology/go-annotation/issues/1544
- https://github.com/geneontology/go-annotation/issues/1674
- https://github.com/geneontology/amigo/issues/43
- https://github.com/geneontology/amigo/issues/295
- https://github.com/geneontology/amigo/issues/440
- Really need a way to identify unsupported ISS annotation (there is no alerting when the primary annotation is removed)
- Block terms not suitable for annotation transfer
examples transporter specificity (changes frequently between species) drug related terms response to terms add examples....
- I would like to propose that we phase out TAS and NAS (not used for future annotations). Should always be an experiment (or an ISO is better than TAS/NAS)
Rules for protein complexes in 'with' column
https://github.com/geneontology/go-ontology/issues/15421
Progress on annotation reviews
Documentation for annotation reviews
Requesting an annotation review tool?
Review existing pages under Quality Control
http://wiki.geneontology.org/index.php/Category:Quality_Control
Meeting notes
- Ask PIs/managers: every contributing group should have one member attending annotation call
- Contributing groups that do not participate must give access to their annotations OR we reserve the right to filter out annotations that do not match our criteria
- Many RCA annotations come from AgBase and Gramene, who haven't responded to our requests