User:A-Kondo

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

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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

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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.

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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

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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

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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

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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

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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.

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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.

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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.

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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.

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.

Datafiles

1.Time-course names

2. Time-course samples ----SampleID, LibraryID

3. FF Ontology file ---- ff-phase2-140729.obo

Linking

1. Time-course → Zenbu (done)

2. Time-course → Sample

3. Sample → FFontology