User:A-Kondo
From FANTOM5_SSTAR
All activities in SSTAR
What:Updates of Sample IDs provided by DDBJ
The target platform:Resource Browser
When:31/July/2014.
How:Run java code
akondo.data.operation.wiki.update.AccessionNumberUpdate.java
What:Updates of Sample IDs provided by DDBJ
The target platform:SSTAR
When:1/August/2014.
How:Run java code
akondo.data.operation.wiki.update.AccessionNumberUpdate.java
What:Fix link on the AccessionId
The target platform:SSTAR
When:4/August/2014.
How:We copy the template(DRAccessionNumber) from RB to SSTAR.
Because the accessionId is linked wrong URL.
As a result, the some accessionId linked to right URL, but some accessionIds remain wrong.
We copy the f5samples template from RB to SSTAR. then the URL linked to DDBJ is fixed.
We found other problems:
1. Why the “LibraryIDs” template is not exist on SSTAR.
2. How to create new Templete on the Media Wiki.
What:Updates of the Timecourse collaborator's name. Replace to name and email link.
The target platform:Resource Browser
When:18/August/2014.
How:Run java code
akondo.data.operation.wiki.update.CollaboratorsEmailUpdate.java
Total time: 2:49.503s
Finished at: Mon Aug 18 14:56:04 JST 2014
Final Memory: 7M/177M
What:Create templete
The target platform:ResourceBrowser
When:12/Sepember/2014.
How:copy the template code of CL to new templates below:
BFO, CHEBI, EFO, GO, IAO, OBI, UO
What:Updates of Ontology pages by javacode using obo file.
The target platform:ResourceBrowser
When:12/Sepember/2014.
How:Run java code akondo.data.operation.ontology.OntologyFix3.java
What:Check Ontology pages.
The target platform:ResourceBrowser
When:16/Sepember/2014.
How:Ontology pages looks good. About the pages that has no ID, we will wait Kasukasa-san or Kawaji-san decide that remove or update the pages before we delete them. The pages are below:
Disposition
MaterialEntity
NCBITaxon
NCBITaxon_10088
NCBITaxon_2759
ProcessualEntity
Role
SpecificallyDependentContinu
What:Update Timecourse Pages(Human)
The target platform:ResourceBrowser
When:16/Sepember/2014.
How: running java class
akondo.data.operation.wiki.update.SPTimeCourseUpdate
1. We remove all human TC pages from RB.
2. Create new TC pages.
The pagenames come from TSV file.
Page contents are copied from old TC pages(Rinderpest).
3. Remove the mouse TC from TSV file and rename it to "new_timecourse_humam.txt".
4. create the TimecourseToSamples_V2_human directory and put the files that include sample id for mouse.
5. Run javacode. After several times trying, the TC page's header looks good, but sample list include old samples.
Short meeting memo(13 Aug 2014)
Serkan-san, Imad-san, Kasukawa-san, A.Kondo
1. LibraryIds template is not exists for SSTAR.
Serkan-san has created the "LibraryIds" template for Resource Browser before his vacation.
But has not created for the SSTAR.
He created the template for SSTAR but it did not work well.
Because "library_id_phase_based" is not exist on SSTAR.
And currently it is not necessary to create "LibraryIds" template for SSTAR.
2. How to create the new template.
To create the new template, open other template and modify the template neme on URL to new template name.
fantom5-collaboration.gsc.riken.jp/resource_browser/Template:new_template_name
You will see the messages that mean the template is not exists.
Click "create" on menu.
The new template will create.
3. Other memo
The Additional Information table on Resource Browser is different from SSTAR.
The "External link for information" in Additional Information table has been added by Serkan-san
that is the latest update for SSTAR. Alistair san requested it.
"External link for information" will be able to be added to Resource browser by copying the template.
The Resource Broswer has more informations than SSTAR,
because the Resource browser is evolving constantly.
And SSTAR's update has been frozen.
Resource Browser should be updated carefully by comparing the both resource.
There are the items that is old and not required.
Meeting memo(14 Aug 2014)
Attendee: Serkan-san, A.Kondo
The discussion is about what is the current request for the phase2.
We have to get the list that includes only phase2 data.
because we have to find the data which should be redirected to phase1 page.
Meeting memo(21 Aug 2014)
Attendee: Imad-san,A.Kondo
Imad-san showed me how to find missing samples.The result is
- 5 samples for human missing in RB
- 513 samples for mm missing in RB.
We will ask Serkan-san tomorrow about the question below:
1. Which class is suitable to update samples using missing samples list(ID & Name).
2. How to create the Timecourse page.
A.Kondo will check the Java class one by one.
Meeting memo(8 Sep 2014)
The OntologyFix3.java is the class for update ontology of SSTAR.
This class requires Onology list and sample id lists.
We already have ontology list but we do not have sample id list.
We need to find how to create the phase2 sampleid list (CL.txt、DOID.txt、FFontology.txt、UBERON.txt).
These are probabry made automatically by java class.
source check after meeting(9/10)
OntologyFix3.java is update the value of "is_a", "derives_from", "part_of", "develops_from", "union_of", "disjoint_from"
in the ff-phase2-140729.obo.
In this class, the CL.txt or DOID.txt or other several files are read but it not used.
1.Time-course names
2. Time-course samples ----SampleID, LibraryID
3. FF Ontology file ---- ff-phase2-140729.obo
1. Time-course → Zenbu (done)
2. Time-course → Sample
3. Sample → FFontology
