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
Copy the "TimeCourse" template source code. And create new template "Time_Course".
Paste the source code to "Time_Course" and save it.
The difference of the "Time_Course" and the "TimeCourse" is just name.
Copy each human and mouse Timecourse page's source code. And save 2 copies to text-file on server.
Remove all the Timecourse pages from Resource browser.
Create new Timecourse pages using the saved text-file on the server.
To create human TC pages, enter the URL for new Timecourse page like: https://fantom5-collaboration.gsc.riken.jp/resource_browser/TimeCourse:XXXXXX Click the "edit" link and paste the source code from the human text-file you saved on server. Before click the save button, update the template name to "Time_Course".
Repeat the new TC page creation for All the human and mouse.
update pagename on excel file.
Copy the discription colomn and paste to pagename column. Imad-san update the pagename to replace "-" to other words.
Run the java code.
Running time is about 90minutes.
What:Change tamplate to show all samples and TC as default.
The target platform:ResourceBrowser
When:28/October/2014.
How:update timecourse template manually.
iDisplayLenght: 10 → -1 aLenghtMenu: [[15, -1], [15, "All"]] → [[-1], ["All"]]
human and mouse use same template.
And the sample template was changed as same as Timecourse template.
What:Update Timecourse pagename.
The target platform:ResourceBrowser
When:29/October/2014.
How:Using java class akondo.data.operation.wiki.update.SPTimeCourseUpdate
For the clearity, we devided the new_timecourse.tsv to the new_timecourse_human.tsv and new_timecourse_mouse.tsv .
We run the program twice for each file, the human and the mouse.
We found the bug on the program that is the "edittoken" has not been taken.
it is requred for the function movepage(), so that we fix the program and re-run it.
The TC list page's reflesh is required to rebuild the list for updated data.
iPS Timecourse should start with the little "i", but It was started with large letter "I".
probably, the small letter is not acceptable on the sematic wiki.
So that we added "Human_" before the iPS Timecourse name.
What:Adjust the column width in the list of Timecourse to show Timecourse name in a single line.
The target platform:ResourceBrowser
When:30/October/2014.
How:update the template of human timecourse list page.
What:Add Overview, Sample description, Quality control to Saos osteosarcoma page.it is sample preview. description date is copied from wiki.
The target platform:ResourceBrowser
When:12/November/2014.
How:Add properties TCOverview, TCSample_description and TCQuality_control to Template:TimeCourse. And add property values to the Saos osteosarcoma page. The description datas are copies from fantom wiki.
What:Phase2 data update from metadata.
The target platform:ResourceBrowser
When:27,28/November/2014.
How:We created new java code for updating sample.
akondo.data.operation.wiki.update.SampleMetadataUpdateforMouse akondo.data.operation.wiki.update.SampleMetadataUpdateforHuman
These code updates using text file Human_sample_metadata.txt mouse_sample_metadata.txt
we have to remove double quotes from these text file. because double quotes on wiki code caused corruption of wiki format.
we started running the code for Human from 27th 4pm to 11pm. The program finished normally. next day we start running the code for Mouse from 28th 9:30am to 11:30pm.
The code running finished normally. We delete one sample below manually.
10005-101B1
At the meeting on afternoon, we found that some samples were not updated correctly.
12250-129H9 12251-129I1 12254-129I4 12255-129I5 12256-129I6
The reason of that was 5 samples on the list on webdav were overlaped. we fix the 5 samples list, and updated them again.
What:Phase2 data update (manual update) Because quality control samples do not appear in the sample list.
The target platform:ResourceBrowser
When:1/December/2014.
How:update 3 samples on browser.
10101-102D2 10101-102D3 10101-102D4
update properties:
sample_categories : tissues → control species : blank → Mouse (Mus musculus)
What:Try combine the files together.
The target platform:
DRA000991.txt
DRA001026.txt
DRA001027.txt
DRA001028.txt
DRA001101.txt
DRA002216.txt
DRA002711.txt
DRA002747.txt
DRA002748.txt
When:1/December/2014.
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
Future query memo(12 Nov 2014)
query test and query result for phase 2 release:
smb://Ascot/lsdm/Resource Browser/Data/phase_2_sample_release
