Difference between revisions of "Contacting the Community"
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/home/postgres/work/pgpopulation/concise_description/20150702_papgenes_after_lastupdate | /home/postgres/work/pgpopulation/concise_description/20150702_papgenes_after_lastupdate | ||
| − | *gene_to_published_after - has a set of WBGenes + locus + count of | + | *gene_to_published_after - has a set of WBGenes + locus + count of papers + list of papers with a gene connection after the gene's date last updated (unsorted, but if you copy the file to your machine and |
| − | papers + list of papers with a gene connection after the gene's date | ||
| − | last updated (unsorted, but if you copy the file to your machine and | ||
put it in excel or something like that, you can sort it) | put it in excel or something like that, you can sort it) | ||
| − | *pis_to_papers_with_genes_published_after - has PIs sorted in | + | *pis_to_papers_with_genes_published_after - has PIs sorted in descending order by count of papers that mention a gene that has a gene connection after the gene's date last updated. So, possibly some papers have multiple genes, but are counted just once. |
| − | descending order by count of papers that mention a gene that has a | ||
| − | gene connection after the gene's date last updated. So, possibly some | ||
| − | papers have multiple genes, but are counted just once. | ||
| − | *This script takes some 40 minutes to run, because we're taking the | + | *This script takes some 40 minutes to run, because we're taking the date last updated, then for each of the 138056 doing a separate query to get paper-gene connections with a timestamp after that. So if we keep working on this script, it'd be kind-of-good to work out what we want since it takes so (relatively) long to run. |
| − | date last updated, then for each of the 138056 doing a separate query | ||
| − | to get paper-gene connections with a timestamp after that. So if we | ||
| − | keep working on this script, it'd be kind-of-good to work out what we | ||
| − | want since it takes so (relatively) long to run. | ||
| − | *Chris has a similar list for newmutant-flagged papers that still need | + | *Chris has a similar list for newmutant-flagged papers that still need curation, so you can both talk about what you want to do next. |
| − | curation, so you can both talk about what you want to do next. | ||
==Letter for Community Annotation== | ==Letter for Community Annotation== | ||
Revision as of 21:27, 18 September 2015
E-mailing the community
On tazendra, in this directory : /home/postgres/work/pgpopulation/concise_description/20150702_papgenes_after_lastupdate
- gene_to_published_after - has a set of WBGenes + locus + count of papers + list of papers with a gene connection after the gene's date last updated (unsorted, but if you copy the file to your machine and
put it in excel or something like that, you can sort it)
- pis_to_papers_with_genes_published_after - has PIs sorted in descending order by count of papers that mention a gene that has a gene connection after the gene's date last updated. So, possibly some papers have multiple genes, but are counted just once.
- This script takes some 40 minutes to run, because we're taking the date last updated, then for each of the 138056 doing a separate query to get paper-gene connections with a timestamp after that. So if we keep working on this script, it'd be kind-of-good to work out what we want since it takes so (relatively) long to run.
- Chris has a similar list for newmutant-flagged papers that still need curation, so you can both talk about what you want to do next.
Letter for Community Annotation
Dear Dr. <name> WormBase appreciates any help it can receive in the form of community annotation, even more so for non-elegans species. We have identified you and your lab as members of the worm community, that can contribute valuable gene function data to WormBase, in the form of free-text, brief gene descriptions. Descriptions will be properly attributed to their authors and displayed on the website. Please use the attached form to submit gene descriptions, the form includes guidelines and other details about how to write them. Thank-you and Regards WormBase Consortium
