Difference between revisions of "First-pass schedule, instructions, automation"

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[[http://www.wormbase.org/wiki/index.php?title=Caltech_documentation&action=submit back]]
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[[Caltech documentation]]<br>
 
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[[First-pass to Curation]]<br>
=[[First-pass data types explained]]=
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[[First-pass_flagging_pipelines]]
[http://www.wormbase.org/wiki/index.php/First-pass_data_types_explained Link to an explanation of the data types as they existed on the old curator firstpass form]
 
 
 
=[[Texpresso/Author/Curator interim form]]=
 
[http://www.wormbase.org/wiki/index.php/Texpresso/Author/Curator_interim_form Link to an explanation of the data types on the new curator form that combines data flagging from all three sources.]
 
 
 
=[http://www.wormbase.org/wiki/index.php/Genetics_Author_pass_form Genetics author first pass form]=
 
  
 
=First-Pass Rotation=
 
=First-Pass Rotation=
 
{| border=2 {{table}}
 
{| border=2 {{table}}
 
| align="center" style="background:#f0f0f0;"|'''First-Pass Curator'''
 
| align="center" style="background:#f0f0f0;"|'''First-Pass Curator'''
| align="center" style="background:#f0f0f0;"|'''Two-week period'''
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| align="center" style="background:#f0f0f0;"|'''Round 1'''
| align="center" style="background:#f0f0f0;"|'''Landmarks'''
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| align="center" style="background:#f0f0f0;"|'''Round 2'''
|-
 
| Karen  ||2/16-3/1||
 
 
|-
 
|-
| Ranjana ||3/2-3/15||
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| Karen  ||2/16-3/1|| 7/6-7/19
 
|-
 
|-
| Raymond ||3/16-3/29||
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| Xiaodong ||3/2-3/15 ||7/20-8/1
 
|-
 
|-
| Jolene ||3/30-4/12|| New forms active
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| Raymond ||3/16-3/29 ||8/3-8/16
 
|-
 
|-
| Gary ||4/13-4/26||Author forms sent out
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| Jolene ||3/30-4/12: New forms active||8/17-8/30
|-
 
| Xiaodong ||4/27-5/10||Author feedback coming in
 
|-
 
| Erich ||5/11-5/24||
 
|-
 
| Wen ||5/25- 6/7||
 
|-
 
| Kimberly ||6/8-6/21||
 
|}
 
 
 
=[http://www.wormbase.org/wiki/index.php/%3DAutomation_progress%3D Automation progress]=
 
DONE = Automated flagging is incorporated into the pipeline and comments show up on the first-pass form.
 
It does not indicate 100% precision or 100% recall.
 
 
 
{| border=2 {{table}}
 
| align="center" style="background:#f0f0f0;"|'''DONE?'''
 
| align="center" style="background:#f0f0f0;"|'''Data Type'''
 
| align="center" style="background:#f0f0f0;"|'''Who'''
 
| align="center" style="background:#f0f0f0;"|'''Notes'''
 
 
|-
 
|-
|||Gene Regulation||Xiaodong/Arun||
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| Gary ||4/13-4/26: Author forms sent out||8/31-9-13
 
|-
 
|-
|'''YES'''||RNAi small scale||Gary/Juancarlos/Ruihua||
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| Ranjana ||4/27-5/10: Author feedback coming in ||9/14-9/27
 
|-
 
|-
|'''YES'''||antibody||Wen/Juancarlos||ready for postgres population 4/8/09
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| Erich ||5/11-5/24||9/28-10/11
 
|-
 
|-
|||allele extraction||Jolene/Arun||
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| Wen ||5/25- 6/7||10/12-10/35
 
|-
 
|-
|||human disease||Ranjana/Juancarlos||
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| Kimberly ||6/8-6/21||10/26-11/8
 
|-
 
|-
|||chemicals/drugs||Karen/Michael/Juancarlos||
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|WormBase re-evalutation||6/22-7/5: IWM||(?)
 
|}
 
|}
  
=Other Tasks=
 
{| border=2
 
  
| align="center" style="background:#f0f0f0;"|'''Who'''
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----
| align="center" style="background:#f0f0f0;"|'''When'''
 
| align="center" style="background:#f0f0f0;"|'''Task'''
 
| align="center" style="background:#f0f0f0;"|'''Goal'''
 
|-
 
|Jolene||current ||with Ruihua: create curation textpresso webpage workspace || automating newmutant sentence identification/extraction for phenotype curation.
 
|-
 
| Wen  ||'''DONE''' ||make foreign language tag for Journals/Articles ||Clear FP list of non-English language articles, which can't be curated
 
|-
 
| Andrei  ||'''DONE'''||Analyze author fill-out form|| To provide a summary of what works and what not and to seek improvements of the procedure.
 
|-
 
| Andrei ||'''DONE'''||Work out the correspondence of fields between the author and curator forms.|||
 
|-
 
| [[Juancarlos]] ||'''DONE'''|| Waiting for consensus on what to put in fields for author and curator for FP.||
 
Raymond suggests : To have a first pass form for curators that shows author's
 
submission for curator's approval (e.g. a tick) for that information to be sent
 
(along with whatever information a curator puts in) for data extraction. If the
 
first-pass curator dis-approves author's input (by not ticking), then the author's
 
input will not be further processed or sent but it will be nevertheless stored as
 
is in the database. For the next phase, results from automated first-pass via
 
textpresso could be treated similarly as that of the author's. The ultimate goal
 
is to maximize the number of fields that need no curator approval. Sources of
 
first-pass curation should be clearly distinguished by a person ID (textpresso
 
will be assigned one).
 
  
Juancarlos is okay with this, but while I'm leaning towards assigning the author
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=Automation=
response to a PersonID, if this is not going to be used for evidence anywhere,
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[http://goldturtle.caltech.edu/wcat/ Textpresso's Automation Explanation and Schedule  http://goldturtle.caltech.edu/wcat/]
the corresponding email is possibly the more accurate evidence since the receiver
 
may pass it on to someone who is not the WBPerson that email is assigned to. In
 
that case Textpresso wouldn't need a person ID. I'm still leaning toward using
 
IDs though, I'm just not sure it reflects the right things if we ever want that
 
in WB or something like that.
 
  
Juancarlos also needs to know how curators want to enter data.  For any given
 
Paper-Field, would curators want to be able to enter unlimited entries, and make
 
then invalid to delete ?  Would you prefer the current system where there's only
 
a single box where everyone mushes in all data ?  Would you care about the history
 
of deleted things ?| 
 
|-
 
|Juancarlos || '''DONE''' || Resolve duplicates || There are many papers on the firstpass list that are already firstpassed. Most of these papers are duplicates and have two WBPaperID assignments. Is there a way to resolve this?.
 
|-
 
|Juancarlos ||'''DONE''' ||Assign Publication Type 'Review' to all papers that are annotated as 'review' in the Comments section of the FP curation form || Remove these papers from the corpus that textpresso searches for data type patterns.
 
|-
 
|Arun||'''DONE''' ||Increase scans for transgene objects to occur daily and change pipeline to run on new papers only|||
 
|-
 
|Juancarlos||'''DONE''' ||Sort papers based on first pass checkout list based on whether or not they have been passed through Textpresso||Curators can now focus on papers whose data fields have already be filled in by textpresso.
 
|}
 
  
==Unassigned tasks and comments that need more discussion==
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----
* We do have a record of data type curation for each paper, is there some way of combining the first pass curation with the curation status form?
 
-The curation status form gets flagged data from the first pass form (don't think I understand the question) -- Juancarlos
 
  
* How does the false positive work?
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=First-pass forms=
- the words ``false positive'' get appended (or prepended, I forget and can't find an example) into the text field -- Juancarlos
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*[http://www.wormbase.org/wiki/index.php/Texpresso/Author/Curator_interim_form New textpresso/author/curator table]
 +
**[http://tazendra.caltech.edu/~postgres/cgi-bin/curator_first_pass.cgi Example of new curator first-pass curation.cgi]
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*[http://www.wormbase.org/wiki/index.php/First-pass_data_types_explained  Old curator first-pass table]
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*[[Author first-pass form]]
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*[[Genetics Author pass form]]
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*[[Data types used on first-pass forms]]
  
* Curator preference for FP remarks, can people deal with the not getting detailed notes about their data type and where it exists in the paper or should this be a mandatory part of first-pass?
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----
  
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=Instructions for curators=
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[http://www.wormbase.org/wiki/index.php/Instructions_for_curators Overview for curators (for the new form)]
  
* Discrepancy between FP papers and total papers curated.  For some data types, curators get to the paper before the FP curator, it would be good to know that a curator already touched it.  Is there a way to mark the paper in the FP list as curated for a specific data type but not others?
 
  
"I have curated some papers that did not go through first pass, mostly Expr_pattern papers published before 2001.
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----
Is it possible that you check current WormBase, find all the paper with Expr_pattern data and flag these papers
 
in postgres as Expr_pattern "yes"?" WC
 
 
"Jolene asked this question last week when she firstpassed an old paper and found that the Expr_patterns she flagged were already curated." JC
 
  
"Sure, please scp a .ace dump with the Expr_pattern and Papers into the
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=Postgres data for individual data types=
  acedb account on tazendra and I'll mark those as ``yes'' (the papers
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*[http://www.wormbase.org/wiki/index.php/FP_curator_comments_for_St.Louis_and_Sanger_structure_correction_data_type St.Louis and Sanger structure correction data type curator comments]
  themselves won't show as already being curated, but will have that
 
  data like the old system worked with textpresso transgene)" JC
 
  
"Would it be possible to do this for all other data types that have been curated from papers that have not gone through first-pass?
 
There are a number of papers that were curated for phenotypes but were not first-passed." KY
 
  
  "Yes.  Likewise generate a .ace file with the data you want, scp it to
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----
  the acedb account on tazendra, and let me know which postgres tables
 
  to populate with that data." JC
 
  
 +
[[User:Kyook|kjy]] 19:43, 9 February 2009 (EST)
  
- I thought on the checkout section they showed as ``RNAi only'' or something like that. -- Juancarlos
 
 
=First-Pass a paper=
 
Access papers on the [http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi WBPaperEditor] page
 
 
==Pick a paper and access the curation form==
 
* Go to http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi
 
* Choose your name
 
* Scroll down the page and select '''"Not Curated Plus Textpresso!"''' ''The body of these papers have passed through Textpresso and should report all found datatypes in the automated pipeline in the appropriate fields.''
 
* Scroll/Page down to a paper and select "Curate!" 
 
 
 
''Alternatively''
 
* Access the curation.cgi from the WBPaperID page itself
 
* Select the WBPaperID from left column to take you to the paper page-- '''ONLY SELECT PAPERS FROM WBPaper0030000 AND LATER'''
 
* Select first-pass curate
 
''Note: the paper pdf can be accessed from the paper page along with supplemental materials.''
 
  
Either action takes you to the curation.cgi (SEE BELOW)
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[[Category:Curation]]
 
 
==New firstpass [http://tazendra.caltech.edu/~postgres/cgi-bin/curator_first_pass.cgi curation.cgi]==
 
 
 
==Old firstpass page [http://tazendra.caltech.edu/~postgres/cgi-bin/curation.cgi curation.cgi]==
 
*At the top of the page are links to:
 
**The tazendra site map (other forms)
 
**Documentation for the set up, paths from, and changes to the curation.cgi form
 
**Guidelines  for the form which include some summary information about the fields and features,  written by Raymond in 2001 and needs some updating.
 
 
 
*For each data type you can check the box or enter text:
 
**Check the box = a '"yes" is entered in to the field
 
**Enter text = the text is recorded
 
 
 
*E-mail is set for default send if there is a "yes" (from a check) or text in the data type flag box.
 
 
 
*When done, you can see the preview of the submission, by selecting "Preview!"
 
**If acceptable,  Select "New Entry!" and flags will be sent to data curators.
 
 
 
'''Saving data''':
 
If you want to come back to the paper later, you can choose to 'Save!' the data.
 
If you do this the next time you 'Load!' the data, ''the form will NOT send flags to curators unless you specify it to do so.''
 
You can restore the default 'send all to curators that have data type info' through the buttons at the top right of the form.
 
 
 
==Adding new gene paper connections==
 
You can add gene paper connections through the WBPaper editor page.  You can search directly for the paper on this page or you can access the paper by hitting "DISPLAY ALL!" and choosing the paper from the left column link.  You will be taken to a summary page for the paper, which at the bottom of the page gives you an area to confirm or add new genes associated with that paper.
 
 
 
 
 
=Automating data type flagging=
 
 
 
===COMPLEX constructions===
 
* Gene Regulation
 
Basically, Arun got training sets from Andrei's first-pass flagged papers. Two training sets include: positive and negative flagged gene-regulation papers. Each set contains about a thousand papers. Then machine will produce index matrices (SVM, support vector machine, more specifically) according to two training sets. Arun can use some representative words/phrases appearing frequently in gene-regulation to fine tune his SVM. A new whole set of papers will be tested and we will see how this works.
 
 
 
* Expression
 
 
 
===SIMPLE patterns===
 
 
 
* RNAi via pattern recognition
 
* Antibody via pattern recognition
 
* Transgene
 
 
 
Pipeline
 
* Pattern Design - Work with Juancarlos and or Michael
 
* Pattern is run on PDFs loaded into postgres. 
 
* Curator gets list of papers that were not picked up by Andrei during first pass to evaluate possible outcomes
 
**are they false positives  - refine pattern
 
**were they missed by Andrei - keep pattern
 
**papers are not true articles and are 'no curatable' - omit from evaluation
 
* Once refined, implement auto population of first pass form for curation
 
* Pattern is run on PDFs loaded into postgres daily. 
 
* Scripts populate first pass form with results from pattern searches.
 
 
 
=[[FP curator comments for St.Louis and Sanger structure correction data type]]=
 
 
 
[[User:Kyook|kjy]] 19:43, 9 February 2009 (EST)
 

Latest revision as of 23:04, 13 August 2010

Caltech documentation
First-pass to Curation
First-pass_flagging_pipelines

First-Pass Rotation

First-Pass Curator Round 1 Round 2
Karen 2/16-3/1 7/6-7/19
Xiaodong 3/2-3/15 7/20-8/1
Raymond 3/16-3/29 8/3-8/16
Jolene 3/30-4/12: New forms active 8/17-8/30
Gary 4/13-4/26: Author forms sent out 8/31-9-13
Ranjana 4/27-5/10: Author feedback coming in 9/14-9/27
Erich 5/11-5/24 9/28-10/11
Wen 5/25- 6/7 10/12-10/35
Kimberly 6/8-6/21 10/26-11/8
WormBase re-evalutation 6/22-7/5: IWM (?)



Automation

Textpresso's Automation Explanation and Schedule http://goldturtle.caltech.edu/wcat/



First-pass forms


Instructions for curators

Overview for curators (for the new form)



Postgres data for individual data types



kjy 19:43, 9 February 2009 (EST)