LEGO May 23, 2016: Difference between revisions
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#RO View for Curators | #RO View for Curators | ||
==GAF/GPAD== | ===GAF/GPAD=== | ||
Still needed before we can import (into MGI): | Still needed before we can import (into MGI): | ||
==Noctua Requirements== | ===Noctua Requirements=== | ||
# Stable purl from which to retrieve files. (GH Noctua issue #200 - https://github.com/geneontology/noctua/issues/200) | # Stable purl from which to retrieve files. (GH Noctua issue #200 - https://github.com/geneontology/noctua/issues/200) | ||
# Folded annotations for individuals annotated by the regulates relation. (GH Noctua issue #189 - https://github.com/geneontology/noctua/issues/189) | # Folded annotations for individuals annotated by the regulates relation. (GH Noctua issue #189 - https://github.com/geneontology/noctua/issues/189) | ||
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# Attribution of curator comments and evidence sentences to the appropriate reference. (https://github.com/geneontology/noctua/issues/280) | # Attribution of curator comments and evidence sentences to the appropriate reference. (https://github.com/geneontology/noctua/issues/280) | ||
Annotation Data flow outstanding Requirements | ===Annotation Data flow outstanding Requirements=== | ||
# Once we have imported annotations into MODs from Noctua, those annotations will be incorporated into output files, GPAD and GAF. Is there a strategy for them not being duplicated when they are picked up by the GOC? | # Once we have imported annotations into MODs from Noctua, those annotations will be incorporated into output files, GPAD and GAF. Is there a strategy for them not being duplicated when they are picked up by the GOC? | ||
# Will annotations in AMIGO2 continue to only come from the 'official providers' or will they be loaded directly? | # Will annotations in AMIGO2 continue to only come from the 'official providers' or will they be loaded directly? | ||
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# What is the order of priority of loaded annotations? When we strip duplicates, which annotations get priority? | # What is the order of priority of loaded annotations? When we strip duplicates, which annotations get priority? | ||
==Discussion of the Wnt signaling model== | ==Annotations/Model Discussion== | ||
===Discussion of the Wnt signaling model=== | |||
http://noctua.berkeleybop.org/editor/graph/gomodel:5716c41300000082 | http://noctua.berkeleybop.org/editor/graph/gomodel:5716c41300000082 | ||
#Explanation of the models and the relations | #Explanation of the models and the relations | ||
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#Is there a mechanism for limiting the annotations that are generated? | #Is there a mechanism for limiting the annotations that are generated? | ||
==Protein Binding Annotations in | ==Protein Binding Annotations in Noctua== | ||
*Use ''has input'' relation for annoton? ''has direct input''? | *Use ''has input'' relation for annoton? ''has direct input''? | ||
**In GAF/GPAD output, this will result in nothing in the With/From column | **In GAF/GPAD output, this will result in nothing in the With/From column | ||
Revision as of 12:29, 20 May 2016
Bluejeans
https://bluejeans.com/969313231
Agenda
Software Updates
- Form Interface for Curation
- RO View for Curators
GAF/GPAD
Still needed before we can import (into MGI):
Noctua Requirements
- Stable purl from which to retrieve files. (GH Noctua issue #200 - https://github.com/geneontology/noctua/issues/200)
- Folded annotations for individuals annotated by the regulates relation. (GH Noctua issue #189 - https://github.com/geneontology/noctua/issues/189)
- Strategy to create regulation target annotations in LEGO
- Annotation of isoforms. Can we start loading GPI files into the NEO.(https://github.com/geneontology/noctua/issues/278)
- Attribution to individual groups. For example 'MGI-Noctua'. (GH Noctua issue #84 - https://github.com/geneontology/noctua/issues/84)
- An automated QC check on annotations made in Noctua. For example, tagging annotations that don't have evidence. (https://github.com/geneontology/noctua/issues/255)
- Attribution of curator comments and evidence sentences to the appropriate reference. (https://github.com/geneontology/noctua/issues/280)
Annotation Data flow outstanding Requirements
- Once we have imported annotations into MODs from Noctua, those annotations will be incorporated into output files, GPAD and GAF. Is there a strategy for them not being duplicated when they are picked up by the GOC?
- Will annotations in AMIGO2 continue to only come from the 'official providers' or will they be loaded directly?
- If annotations cycle through the 'official providers', then the official providers should all be encouraged to load GPAD files so that the associated annotation properties in column 12 of the GPAD file are not lost. How important is this since we have the original OWL saved?
- What is the order of priority of loaded annotations? When we strip duplicates, which annotations get priority?
Annotations/Model Discussion
Discussion of the Wnt signaling model
http://noctua.berkeleybop.org/editor/graph/gomodel:5716c41300000082
- Explanation of the models and the relations
- How will the individuals in the model chain?
- What annotations do we expect to get from a model like this?
- Is there a mechanism for limiting the annotations that are generated?
Protein Binding Annotations in Noctua
- Use has input relation for annoton? has direct input?
- In GAF/GPAD output, this will result in nothing in the With/From column
- Use With/From column only?
- Use both?