NOV 11 2010

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*Java based solution for filling up cvtermpath table(transitive closure of relationships). Triggered from a discussion in gmod mailing list. *Java based solution for filling up cvtermpath table(transitive closure of relationships). Triggered from a discussion in gmod mailing list.
:Doing with the help of C.Mungall. :Doing with the help of C.Mungall.
-:Target is to do OWL -> closure dump -> load in chado.+:Target is to do OWL -> closure dump -> load in chado. DELAY until complex ontology searches are tied into search update.
 +*After new OBO file upgrade, curators (with help of Sidd) need to check where terms don't map and map manually.
 +*GO tool: Use EBI tool, curators prepare for using this tool in December.
 + 
;Interpro domains for all dicty genes (Yulia) ;Interpro domains for all dicty genes (Yulia)
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=== DONE === === DONE ===
 +
;Link to ENSEMBL [Yulia] ;Link to ENSEMBL [Yulia]
:Our links from the genome browse don't work anymore (at least for me - Petra), e.g. [http://dictybase.org/db/cgi-bin/ggb/gbrowse/dictyBase/?name=5%3A1638497..1642140 ]. And it would be nice to link to the EnsemblProtists from our gene pages. Example link, [http://protists.ensembl.org/Dictyostelium_discoideum/Gene/Summary?g=DDB_G0288511] :Our links from the genome browse don't work anymore (at least for me - Petra), e.g. [http://dictybase.org/db/cgi-bin/ggb/gbrowse/dictyBase/?name=5%3A1638497..1642140 ]. And it would be nice to link to the EnsemblProtists from our gene pages. Example link, [http://protists.ensembl.org/Dictyostelium_discoideum/Gene/Summary?g=DDB_G0288511]
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Action: extended cookies lifespan to 3 month (was set to expire with session end), Added shopping card to all SC pages Action: extended cookies lifespan to 3 month (was set to expire with session end), Added shopping card to all SC pages
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 +
 +==Gene page caching==
 +* We have the cached gene pages now for 7 days, but the limit to 7 days only makes sense if there is a script that refreshes and therefore caches all gene pages every weekend. Otherwise, if the regular user goes to their gene very Friday or so, nothing is gained for them with the 7 day expiration alone (Petra)
==Expression Data from Harry== ==Expression Data from Harry==

Current revision

Contents

Next release 2.19 (Dec. 17th)

Working on

Migrating reference tables and GO to Chado
  • Migrate the reference search. [Done]
  • Migrate the batch reference update script. [Done]

[Working on]

  • Scripts for import and update of OBO files.
  • Java based solution for filling up cvtermpath table(transitive closure of relationships). Triggered from a discussion in gmod mailing list.
Doing with the help of C.Mungall.
Target is to do OWL -> closure dump -> load in chado. DELAY until complex ontology searches are tied into search update.
  • After new OBO file upgrade, curators (with help of Sidd) need to check where terms don't map and map manually.
  • GO tool: Use EBI tool, curators prepare for using this tool in December.


Interpro domains for all dicty genes (Yulia)
Run whole pipeline couple of times to test
Automate curation stats -Excel (Yulia)
should it be available for users to see?

DONE

Link to ENSEMBL [Yulia]
Our links from the genome browse don't work anymore (at least for me - Petra), e.g. [1]. And it would be nice to link to the EnsemblProtists from our gene pages. Example link, [2]

working link for EmsemblProtists for GBrowse http://protists.ensembl.org/Dictyostelium_discoideum/Location/View?db=core;r=1:1000-30000

Action: wrote patch that adds Ensembl linkouts for genes. Used the same gff3 as they used for import (10-14-2009)

Fix Pseudogene - Gene association bug [Yulia]
Pseudogene features cannot be associated with another gene, which needs fixing. See issue [3] [Petra]
Link outs to GenBank [Yulia]

The GenBank links on the Gene pages (see for example sadA gene) we link out to our own version of the sequence (for example sadA AY178767). This is misleading and also unnecessary. We should link to GenBank directly and remove the tab for the GenBank sequence.

Action: fixed gene page and gbrowse links, removed genbank features from sequence dropdown in BLAST

Stock Center User requests (Yulia) [Done]
  • Add shopping cart to each strain and plasmid page.
    • SC search pages
    • strain catalog
    • strain page
  • Make shopping cart 'sticky' so it remembers what's in it.

Action: extended cookies lifespan to 3 month (was set to expire with session end), Added shopping card to all SC pages


Gene page caching

  • We have the cached gene pages now for 7 days, but the limit to 7 days only makes sense if there is a script that refreshes and therefore caches all gene pages every weekend. Otherwise, if the regular user goes to their gene very Friday or so, nothing is gained for them with the 7 day expiration alone (Petra)

Expression Data from Harry

  • Harry sent expression, spatial and temporal, plus cell cycle regulation data, in an Excel sheet with Macros. User request
  • We should have a look at the data table and make a plan when and how we can use it.
  • I can visualize the graphs (not so elegantly because I can't have Macros on the Mac) and it would be great to have those linked to genes. Here is a screenshot of what the graphs look like Image:Harry_graphs.png



Separating floatigs

Do we still have plans to do that? Maybe independent of that, I found a short contig in the 2F concatemer (DDB0215024), that's for sure a duplicate of an integrated chr 2 region. There were 4 genes on the contig of which two were tiny I deleted those, DDB_G0294182 (7 aa), DDB_G0294184 (21 aa - conserved piece occuring in 7 genes on chr 2,3 and 5). Then there are two genes that are predicted exactly like on chr2: DDB_G0271418/DDB_G0294188 and DDB_G0271416/DDB_G0294186. I blasted the genomic sequence and there are 7 mismatches, mostly at the ends of the small 2F contig, but I definitely think these are redundant. [Petra]

IntAct

Intact- Uniprot export files


On 9/28/10 4:50 PM, Samuel Kerrien wrote:

Brilliant, do get in touch again if we can help further.
Cheers

Sam

On 28 September 2010 15:09, Pascale Gaudet <pgaudet@northwestern.edu> wrote:

Dear Sam,
I can't find a reply to this email - but I wanted to let you know we have discussed 
the UniProt export files and we can use them to integrate the IntAct data into dictyBase.
Best regards,

Pascale
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