Annotation Conf. Call 2022-08-30: Difference between revisions
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(Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - '''PLEASE REGISTER by SEPT. 1st''' ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group to...") |
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Line 86: | Line 86: | ||
* PomBase 5 | * PomBase 5 | ||
* RGD 22 | * RGD 22 | ||
* SGD 103 | * SGD 103 - done | ||
* SynGO 82 | * SynGO 82 | ||
* SynGO-UCL 3 | * SynGO-UCL 3 |
Revision as of 15:19, 29 August 2022
Agenda and Minutes
Meetings and Announcements
Fall 2022 Consortium Meeting
- In person with remote accommodation
- At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th
- Registration form - PLEASE REGISTER by SEPT. 1st
- See agenda for pswd
- Please think about agenda items and breakout group topics
Noctua
- Next regularly scheduled Noctua outage:
- Thursday, September 8th
GO Release Pipeline
- August release still pending (but passed QC inspection)
Tracker summary emails for go-ontology and go-annotation
- From Seth: It has come to our notice that due to an issue we are having with our email delivery system (https://github.com/geneontology/go-site/issues/1891), we have been unable to send summaries since the 12th. As a stopgap measure until this issue has been fixed, we will manually send these emails on Fridays on a weekly interval, starting tomorrow. We hope to have a permanent resolution to this quickly and return to the previous daily summaries.
AmiGO
Ontology
Membrane CC Terms
Remaining: Extrinsic component of membrane Cannot be sure whether these were membrane or membrane-associated, so we need to obsolete with 'consider' the parent term
- extrinsic component of membrane 120
- extrinsic component of cytoplasmic side of plasma membrane 98
- extrinsic component of plasma membrane 70
- extrinsic component of mitochondrial inner membrane 38
- extrinsic component of synaptic vesicle membrane 22
- extrinsic component of endoplasmic reticulum membrane 19
- extrinsic component of mitochondrial outer membrane 19
- extrinsic component of postsynaptic membrane 16
- extrinsic component of external side of plasma membrane 13
- extrinsic component of presynaptic membrane 13
- extrinsic component of endosome membrane 10
- extrinsic component of postsynaptic density membrane 9
- extrinsic component of fungal-type vacuolar membrane 8
- extrinsic component of synaptic membrane 8
- extrinsic component of Golgi membrane 5
- extrinsic component of presynaptic endocytic zone membrane 5
- extrinsic component of neuronal dense core vesicle membrane 5
- extrinsic component of periplasmic side of plasma membrane 4
- extrinsic component of vacuolar membrane 4
- extrinsic component of postsynaptic specialization membrane 4
- extrinsic component of organelle membrane 4
- extrinsic component of autophagosome membrane 3
- extrinsic component of intraperoxisomal membrane 3
- extrinsic component of presynaptic active zone membrane 3
- extrinsic component of omegasome membrane 3
- extrinsic component of plastid membrane 3
- extrinsic component of lysosome membrane 2
- extrinsic component of postsynaptic endosome membrane 2
- extrinsic component of stromal side of plastid thylakoid membrane 2
- extrinsic component of phagophore assembly site membrane 2
- extrinsic component of cell outer membrane 1
- subplasmalemmal coating 1
- extrinsic component of nuclear outer membrane 1
- extrinsic component of matrix side of mitochondrial inner membrane 1
- extrinsic component of postsynaptic early endosome membrane 1
- extrinsic component of thylakoid membrane 1
By group:
Contributor (Assigned by)
- AgBase 2
- ARUK-UCL 6
- BHF-UCL 13
- CACAO 2
- CAFA 1
- CGD 1
- ComplexPortal 3
- dictyBase 6
- EcoCyc 21
- EcoliWiki 6
- FlyBase 18
- GeneDB 4
- GO_Central 3
- MGI 27
- ParkinsonsUK-UCL 4
- PomBase 5
- RGD 22
- SGD 103 - done
- SynGO 82
- SynGO-UCL 3
- TAIR 26
- UniProt 157
- WB 3
- ZFIN 5
Annotation
Review of histone modification annotations
- Annotation review ticket: https://github.com/geneontology/go-annotation/issues/4261
- Annotation review spreadsheet: https://docs.google.com/spreadsheets/d/1LJTu3sZjwH7u3sD65KXf_e-l3A85cRKpeiYh2DVsRgg/edit#gid=1052081963
- Grouped by
- Is in a Panther family that is one of the 134 enzymes? -> yellow
- made a list of the '623 enzymes' sheet: https://docs.google.com/spreadsheets/d/1LJTu3sZjwH7u3sD65KXf_e-l3A85cRKpeiYh2DVsRgg/edit#gid=909564179
Remaining enzymes to review (according to the spreadsheet):
- ARUK-UCL 2
- BHF-UCL 9
- CACAO 17
- CAFA 1
- CGD 5
- ComplexPortal 17
- dictyBase 1
- FlyBase 108
- HGNC 3
- HGNC-UCL 2
- MGI 95
- PomBase 3
- RGD 9
- SGD 48
- UniProt 35
- WB 42
- ZFIN 24
The [Annotation review ticket https://github.com/geneontology/go-annotation/issues/4261] also has spreadsheets for dbTFs, coTFs and GTFs
Annotation error reports and annotation review
- Please remember to keep checking the reports generated by the pipeline and address any errors
- Also check annotation review tickets assigned to you/your group in go-annotation repo on github
- Questions about either - please bring to the meeting
GO-CAM and Noctua
Other Projects
Attendees
- On call: