[Treebase-guts] [ treebase-Bugs-2826165 ] Reviewer/Referee Access

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Bugs item #2826165, was opened at 2009-07-23 15:36
Message generated for change (Comment added) made by sfrgpiel
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Category: ui
Group: None
Status: Open
Priority: 8
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: Reviewer/Referee Access

Initial Comment:
I'm making this a priority of 9 only because it is needed before TreeBASE2 can be made public. We need to make sure that reviewers or referees can have access to datasets that are "in progress" and associated with a manuscript that is in the review process of a journal. Jin Ruan initially created a user role called "reviewer" which gives someone read-only access to the private sections of the database. We decided that this is a bad solution because it requires that each reviewer get a login name and password, which implies a huge amount of admin overhead. A better solution is to auto-generate a long random string which can be used in an URL to give someone a read-only access to the submission page. But however which way we do this, it is needed because some journals depend on this as part of their review process.

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>Comment By: William Piel (sfrgpiel)
Date: 2009-12-10 19:37

Message:
Here are some more comments on how I envision this feature -- but of course
I'm open to input from everyone regarding this. 

The basic requirement is that the submitter gets either a PIN or an URL
for each submission/study that s/he initiates. This should be provided to
the submitter at the submission summary page. For example, here is the
"summary" page that a submitter might see:

http://treebasedb-dev.nescent.org:6666/treebase-web/user/summary.html?id=1937

... in this case, the submission is "published" so it is visible to
everyone -- but in the event that the submission was "in progress" or
"ready," only the submitter or an administrator can view the submission. In
the "Summary" box that you can see after following the url (above), we
currently have the following items: 

(1) submission id
(2) the date submission initiated
(3) citation
(4) abstract

For submissions regardless of status, we should add the following:

(a) the date last modified
(b) the following statement: "To cite your data in a paper or other data
resources, please use the following Universal Resource Identifier (URI):
http://purl.org/phylo/treebase/phylows/study/TB2:S1936"

For submissions that are "in progress" or "ready," we should add the
following:

(c) "Until your submission status is change to "published," your data will
remain invisible to everyone except you, TreeBASE staff, and anyone who
uses your URI together with a unique "x-reviewer_pin" parameter. To provide
journal editors or reviewers of your paper with advanced access to your
data, please email the following URL to them:

http://purl.org/phylo/treebase/phylows/study/TB2:S1936?x-reviewer_pin=1234567890&format=html

This URL contains the unique x-reviewer_pin parameter that provides
read-only access to your data. It is recommended that you provide this to
your editor or reviews only after your submission is complete."

So... for this to work we need to modify Rutger's phylows code to read the
extra parameter "x-reviewer_pin" and to use this to give anonymous access
to the corresponding submission even though its status is "in progress" or
"ready." My guess is that this would involve generating a cookie so that
once the user's browser resolves the phylows + x-reviewer_pin URL, the
reviewer can continue clicking on the related analysis, matrix, tree, and
taxa tabs. Additionally, the cookie allows the reviewer to download
matrices and trees for this study. 

How should we generate the PIN? One way is to add a new field to the study
table to store a randomly-generated PIN. But that means modifying the
schema, which is probably not ideal. Another way is to generate an md5 on,
for example, a concatenation of the study_id and the date that the
submission was first created. 

The other thing that would be good is that when the reviewer first follows
the phylows + x-reviewer_pin URL, he/she is confronted with an "agreement"
page or pop-up. This "agreement" page or popup contains an "Accept" and a
"Cancel" button. The Cancel button closes out the browser page. The
"Accept" button continues to the submission.  The verbiage for this
"agreement" page is written below. 

regards,

Bill

=====================
Reviewer/Referee Access Agreement

You have reached this page using a PIN that is intended to be used by
journal editors and reviewers or referees of a paper that is under
consideration for publication. This PIN gives you access to the submitted
data and metadata associated with analyses and results presented in the
paper under review. Please carefully examine the data paying special
attention to the following:

- The citation data (authors, year, citation, abstract) should be
complete, except for information that is not yet known (e.g. volume or page
numbers). 
- Verify that nexus files are error-free and executable by software
programs (e.g. PAUP, Mesquite, MacClade, etc). Please make sure that the
taxon labels for trees are identical, or a subset of, the taxon labels in
data matrices connected by way of an analysis. If taxon labels in trees do
not match with taxon labels in associated data matrices, the data will not
be useful to the scientific community.
- Verify that data are not missing and that opportunities to supply
valuable metadata are not overlooked. For example, TreeBASE can store
Genbank accession numbers, museum voucher IDs, latitude and longitudes for
specimen localities, character names and character state names for
morphological data, etc. Including these metadata are sometimes overlooked
by submitting authors, yet sharing this metadata is extremely valuable to
the scientific community. Please use your power as a reviewer to encourage
the sharing of richly-annotated metadata. 
- Verify that analyses are not missing and that, where possible, analysis
entries include software commands (e.g. the contents of a PAUP block or
MrBayes block) so that analyses can be replicated easily (e.g. commands
that describe substitution models, data partitions, and heuristic search
parameters).
- Verify that taxon labels are mapped against TreeBASE's taxonomic
dictionary. Data in TreeBASE can only be found using a taxon name search if
the taxon labels are properly mapped. 

By clicking the "Accept" button below, you agree to keep these data
confidential; you agree not retain these data after completing your report
to the journal editor; you agree not use these data or knowledge of these
data for the purposes of your research until and unless the paper under
review has been published and the data have been made available to the
general public; you agree to keep the PIN confidential.



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