Feature Requests

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Feature Requests

Curation analysis features

• Concerning the "Comment" data field

1. Change "Comment" button at the bottom of the form to "All Comments".
2. Filter out all records where author form has value "some comment" AND Curator form has "review" or "nocuratable". If Curator form has either of these comments but Author form is not blank but has something other than "some comment" show all comments for that paper.
3. Sort by WBPaper ID in reverse order.

• Make a new button called "No Curatable Comments" for all the comments in the nocuratable table.

Other Tasks

Who	When	Task	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 response to a PersonID, if this is not going to be used for evidence anywhere, 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

• 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?

- the words ``false positive get appended (or prepended, I forget and can't find an example) into the text field -- Juancarlos

• 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?

• 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. 
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
 acedb account on tazendra and I'll mark those as ``yes (the papers
 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
 the acedb account on tazendra, and let me know which postgres tables
 to populate with that data." JC

- I thought on the checkout section they showed as ``RNAi only or something like that. -- Juancarlos