Difference between revisions of "WormBase-Caltech Weekly Calls"
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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]] | [[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]] | ||
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| + | [[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]] | ||
GoToMeeting link: https://www.gotomeet.me/wormbase1 | GoToMeeting link: https://www.gotomeet.me/wormbase1 | ||
| + | = 2020 Meetings = | ||
| − | = | + | == January 9, 2020 == |
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| − | + | === Phenotype Curation Requests === | |
| + | * 1,229 emails sent Dec 3-6, 2019 | ||
| + | * Received 194 annotations from 40 papers and from 37 distinct community curators | ||
| + | ** 37 papers requested, 3 additional papers annotated | ||
| + | ** 104 Phenotype OA annotations (from 27 papers; 25 distinct curators) | ||
| + | ** 90 RNAi OA annotations (from 20 papers; 19 distinct curators) | ||
| + | * 43 bounced emails | ||
| + | ** 2 resent to new addresses | ||
| + | ** 5 have backup email addresses (also sent) | ||
| − | + | === Worm Area Meetings === | |
| + | * Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting | ||
| + | * Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest) | ||
| − | [ | + | === Reference widget Textpresso linkouts === |
| + | * Now live on WormBase, WS274 | ||
| + | * [https://github.com/WormBase/website/issues/7347 GitHub ticket] | ||
| + | * Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes | ||
| + | * Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10 | ||
| + | * Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10 | ||
| + | * Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10 | ||
| + | * Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10 | ||
| + | ** Known issue: searching on synonyms in addition to public name; Sibyl will fix | ||
| + | * Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10 | ||
| + | ** Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix | ||
| + | * Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10 | ||
| + | ** Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell | ||
| + | * Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10 | ||
| + | * Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10 | ||
| + | ** Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym | ||
| + | * Rearrangement example: https://wormbase.org/species/all/rearrangement/sDp3#03--10 | ||
| + | * Molecule example: https://wormbase.org/resources/molecule/WBMol:00003650#03--10 | ||
| + | * Process examples: | ||
| + | ** https://wormbase.org/resources/wbprocess/WBbiopr:00000001#09--10 | ||
| + | ** https://wormbase.org/resources/wbprocess/WBbiopr:00000079#09--10 | ||
| + | * Michael has improved phrase search and combined supplemental documents with main paper documents; should roll out soon | ||
| − | + | === WS276 Citace upload === | |
| + | * Hinxton upload Jan 31, 2020 | ||
| + | * Citace upload on Tuesday, Jan 28, 2020 | ||
| − | + | === Author First Pass paper === | |
| + | * AFP resent to Database | ||
| + | * Automated descriptions about to be sent | ||
| + | * SObA, write for micropub? One micropub on SObA and another on comparative SObA | ||
| − | + | === Noctua/GO-CAM === | |
| + | * New version of the Noctua form released next week | ||
| + | * Imports from WormBase? | ||
| + | ** Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track) | ||
| + | ** Need to work on annotation history on back end | ||
| + | ** May have face-to-face meeting in Pasadena | ||
| − | + | === Variation curation === | |
| + | * Have a backlog; Paul D is assigned but has been overwhelmed | ||
| + | * Have asserted this as a priority | ||
| + | * We have the allele-sequence form; where does it go? Hinxton | ||
| + | * Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance | ||
| + | * Need to integrate curation with the Variant Effect Predictor (VEP) pipeline | ||
| + | === Topic meetings === | ||
| + | * Asia (Taipei) meeting, Paul S going | ||
| + | * Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.) | ||
| + | * TAGC in April, Chris going | ||
| − | |||
| − | == | + | == January 16, 2020 == |
| − | |||
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| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | === | + | === Variation names === |
| − | * | + | * Daniela entered a new allele name (tkTi1) in the temporary allele form CGI but it prompted an error: tkTi1 does not match 1 or 2 sets of 1-3 letters and 1-6 digits
. |
| − | * | + | * Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3. |
| − | * | + | * Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo |
| − | * | + | * From the nomenclature guidelines: Newly generated Transposon insertions, especially those located in apparently intergenic regions, may also be given Ti (transposon insertion) names. These consist of the designation identifying the laboratory of origin, the two letters Ti, and a number, all italicized. Example: eTi13 is an insertion of a Mos transposon into an intergenic region on LGIII. |
| + | * We will wait for Paul D/Tim response and act accordingly | ||
| + | * for now the CGI has been changed to allow 4 letters, we will revert if need be | ||
| − | === | + | === Webinars === |
| − | * | + | * During an AFP call we discussed the possibility to have webinars for authors to guide them through the form. |
| − | * | + | * Is having a webinar series something WB is interested in doing? |
| − | * | + | ** we will start with an AFP/micropub webinar and will take it from there based on interest and attendance |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| + | == January 23, 2020 == | ||
| − | == | + | === WS276 Citace upload === |
| + | * Next Tuesday, Jan 28 10am Pacific | ||
| − | === | + | === Extracellular/secreted proteins list === |
| − | * | + | * Peter Roy looking for a list of C. elegans genes whose protein products are secreted |
| − | * | + | * Chris pointed him to BioMart search for SignalP and transmembrane proteins, and to the GO term page for "extracellular region" but Peter doesn't think that's exhaustive enough |
| − | + | * Does anyone have any other suggestions or know of an empirical data set? | |
| − | + | * A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome: https://www.ncbi.nlm.nih.gov/pubmed/22823938 | |
| − | + | * PF00188 Cysteine-rich secretory protein family Pfam | |
| − | + | ** This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes [PMID:12625841] | |
| − | * | ||
| − | * | ||
| − | |||
| − | * | ||
| − | * | ||
| − | |||
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Revision as of 19:18, 23 January 2020
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2020 Meetings
January 9, 2020
Phenotype Curation Requests
- 1,229 emails sent Dec 3-6, 2019
- Received 194 annotations from 40 papers and from 37 distinct community curators
- 37 papers requested, 3 additional papers annotated
- 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
- 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
- 43 bounced emails
- 2 resent to new addresses
- 5 have backup email addresses (also sent)
Worm Area Meetings
- Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
- Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)
Reference widget Textpresso linkouts
- Now live on WormBase, WS274
- GitHub ticket
- Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes
- Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10
- Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10
- Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10
- Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10
- Known issue: searching on synonyms in addition to public name; Sibyl will fix
- Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10
- Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix
- Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10
- Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell
- Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10
- Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10
- Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym
- Rearrangement example: https://wormbase.org/species/all/rearrangement/sDp3#03--10
- Molecule example: https://wormbase.org/resources/molecule/WBMol:00003650#03--10
- Process examples:
- Michael has improved phrase search and combined supplemental documents with main paper documents; should roll out soon
WS276 Citace upload
- Hinxton upload Jan 31, 2020
- Citace upload on Tuesday, Jan 28, 2020
Author First Pass paper
- AFP resent to Database
- Automated descriptions about to be sent
- SObA, write for micropub? One micropub on SObA and another on comparative SObA
Noctua/GO-CAM
- New version of the Noctua form released next week
- Imports from WormBase?
- Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
- Need to work on annotation history on back end
- May have face-to-face meeting in Pasadena
Variation curation
- Have a backlog; Paul D is assigned but has been overwhelmed
- Have asserted this as a priority
- We have the allele-sequence form; where does it go? Hinxton
- Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
- Need to integrate curation with the Variant Effect Predictor (VEP) pipeline
Topic meetings
- Asia (Taipei) meeting, Paul S going
- Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.)
- TAGC in April, Chris going
January 16, 2020
Variation names
- Daniela entered a new allele name (tkTi1) in the temporary allele form CGI but it prompted an error: tkTi1 does not match 1 or 2 sets of 1-3 letters and 1-6 digits .
- Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3.
- Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
- From the nomenclature guidelines: Newly generated Transposon insertions, especially those located in apparently intergenic regions, may also be given Ti (transposon insertion) names. These consist of the designation identifying the laboratory of origin, the two letters Ti, and a number, all italicized. Example: eTi13 is an insertion of a Mos transposon into an intergenic region on LGIII.
- We will wait for Paul D/Tim response and act accordingly
- for now the CGI has been changed to allow 4 letters, we will revert if need be
Webinars
- During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
- Is having a webinar series something WB is interested in doing?
- we will start with an AFP/micropub webinar and will take it from there based on interest and attendance
January 23, 2020
WS276 Citace upload
- Next Tuesday, Jan 28 10am Pacific
Extracellular/secreted proteins list
- Peter Roy looking for a list of C. elegans genes whose protein products are secreted
- Chris pointed him to BioMart search for SignalP and transmembrane proteins, and to the GO term page for "extracellular region" but Peter doesn't think that's exhaustive enough
- Does anyone have any other suggestions or know of an empirical data set?
- A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome: https://www.ncbi.nlm.nih.gov/pubmed/22823938
- PF00188 Cysteine-rich secretory protein family Pfam
- This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes [PMID:12625841]
