September 26 & 27, 2011
September 26 & 27, 2011
Feb 26, 2016
September 26 & 27, 2011. No Smoking!. (yes, they are serious about this). Facilities. Restrooms at the ends of the hall and upstairs. Lunch will be on your own. The Natcheteria is upstairs, and they have been warned that we are here. Details on box lunches will come. - PowerPoint PPT Presentation
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September 26 & 27, 2011
No Smoking!(yes, they are serious about this)
Facilities• Restrooms at the ends of the hall and upstairs.• Lunch will be on your own. The Natcheteria is
upstairs, and they have been warned that we are here. Details on box lunches will come.
• Coffee Breaks will be in the back of the room (and most likely spilling out into the hall).
• Parking• We are close here, so please be a good
neighbor.
Program
• Opportunities for questions and discussion after each presentation.
• Please use the microphones.• And tell us who you are.
• There will be an open session on Tuesday afternoon. Bring your suggestions, questions, and gripes.
Thank You to the Peer Reviewers
• Steve DeRose• Jeff Fisher• Daniel Grossberg• Mirko Janc• Sheila Morrissey• Evan Owens• Bruce Rosenblum• Sasha Schwarzman• Kim Tryka
And to the Program Committee
• Laura Kelly• Deborah Lapeyre• B. Tommie Usdin
(Who were also peer reviewers)
September 26 & 27, 2011
Interesting things that have happened since we last met
• NISO Z39.96 JATS version 0.4 was released as a Draft Standard for Trial Use on March 30, 2011
• NCBI hosted a meeting in August 2011 to update the NCBI Book DTD
NISO JATS version 0.4
• Release March 30, 2011.• As a Draft Standard for Trial Use• 6-month comment period ends September 30• Project name has shifted from “NLM DTD” to
“Journal Article Tag Suite (JATS)” or “NISO JATS”
Why the name change?• Because the standard doesn't define a “DTD”
it defines a set of XML elements and attributes and three Article models (Tag Sets) in plain text: - Archiving and Interchange Tag Set,- Journal Publishing Tag Set- Article Authoring Tag Set.
• Coincidentally, these Tag Sets correspond to the three “old NLM DTDs”- Archiving and Interchange DTD,- Journal Publishing DTD- Article Authoring DTD.
In plain text?
New home for JATS files at NLM
• New home website created for the NISO JATS non-normative supporting documents:
http://jats.nlm.nih.gov
This site includes schema versions (DTD, XSD, RNG) for each of the Tag Sets along with the documentation (Tag Library) for each.
http://jats.nlm.nih.gov/publishing/0.4/JATS-journalpublishing0.dtd
http://jats.nlm.nih.gov/publishing/tag-library/0.4
And dtd.nlm.nih.gov?
• Still includes all documentation for older versions, NLM DTD 1.0 through 3.0.
• At the Tag Set level, the old site and new site are linked together pretty well.
What happens next?
After the Comment Period closes on September 30, the NISO Working Group will address all comments and produce a new version of the Standard Document (NISO JATS 1.0) along with all of the non-normative supporting documents (schemas and documentation).
Important Conference Info!
Any suggestions that come from the floor of this meeting will not be considered official comments.
(similarly for any suggestions made to one of the Working Group members in the hall or in an email or in a note passed at recess.)
All comments must be made through the NISO website to be considered by the Working Group http://www.niso.org/apps/group_public/document.php?document_id=6135).
• Then Version 1.0 will be voted on by the NISO members.
• The Standard will be in Continuous Maintenance, which means we will continue to accept comments from users and continue to update the Standard Document and the Supporting Documentation.
The Book Model
• NCBI hosted a meeting in August 2011 to update the NCBI Book DTD.
• The goal was to build a general book model from the JATS.
Some decisions included:
• The new book model is not intended for ALL books. – Technical monographs, government
reports, multivolume monographic series, reference books, encyclopedias, college-level textbooks, and professional books were all declared to be in scope.
– Children's books, legislative materials, scripture and sacred literature, dictionaries, magazine-like books, and K-12 textbooks were all declared to be out of scope.
• Like the JATS, the New Book Model will focus on tagging content rather than formatting or layout.
• The new model is intended for publishers who have journal content in JATS who wish to tag their book content in a similar way.
• A book "chapter" body is very similar in structure to a journal article body.
• The book model will use the same structures and element names from JATS where it makes sense.
• Books may exist as a single XML document or a collection of book-part- (e.g. chapter)-level documents.
• The book model will be based on NISO JATS 1.0(so, it will not be released until AFTER NISO Z39.96 JATS 1.0 is official)
March 2003
NLM
DTDs v 1.0
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
This was when the Article Archiving and Journal Publishing models became more open and we added the Authoring model.
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
Decision to formalize standard with NISO
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
NLM
DTDs v 3.0N
ovember 2008
Backward-incompatible release
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
NLM
DTDs v 3.0N
ovember 2008
Backward-incompatible release
NLM
DTDs v 3.1
NLM DTD Working Group is dissolved, and the NISO Journal Article Tag Suite Working Group is created.
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
NLM
DTDs v 3.0N
ovember 2008
Backward-incompatible release
NISO
Z39.96 JATS v 0.4M
arch 2011
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
NLM
DTDs v 3.0N
ovember 2008
Backward-incompatible release
NISO
Z39.96 JATS v 0.4M
arch 2011
September 30, 2011
End of public comment period
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
NLM
DTDs v 3.0N
ovember 2008
Backward-incompatible release
NISO
Z39.96 JATS v 0.4M
arch 2011
September 30, 2011
End of public comment period
FUTURE!
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
NLM
DTDs v 3.0N
ovember 2008
Backward-incompatible release
NISO
Z39.96 JATS v 0.4M
arch 2011
September 30, 2011
End of public comment period
FUTURE!
NISO
Z39.96 JATS v 1.0
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
NLM
DTDs v 3.0N
ovember 2008
Backward-incompatible release
NISO
Z39.96 JATS v 0.4M
arch 2011
September 30, 2011
End of public comment period
FUTURE!
NISO
Z39.96 JATS v 1.0
March 2003
NLM
DTDs v 1.0N
ovember 2003
NLM
DTDs v 1.1
Novem
ber 2004 N
LM DTDs v 2.0
September 2005
NLM
DTDs v 2.1
NLM
DTDs v 2.2June 2006
NLM
DTDs v 2.3M
arch 2007
NLM
DTDs v 3.0N
ovember 2008
Backward-incompatible release
NISO
Z39.96 JATS v 0.4M
arch 2011
September 30, 2011
End of public comment period
FUTURE!
NISO
Z39.96 JATS v 1.0
Expect to release new NCBI/NLM Book Model just after NISO JATS 1.0 is released
What’s the new book model called?
• Some names either considered and rejected or not considered:– JATSBook– DocJATs– BATS– Buttercup
• Book Interchange Tag Suite (BITS)
Best Practices or Common Practice?
• Sometimes people want to be told what to do.
• Working on the JATS project, we get a lot of requests for "Best Practices”
“How do I tag …?”
• But what are you asking for when you are asking for “Best Practices”?
• And how do you feel about someone who knows what’s best for you?
• The JATS Tag Sets - especially the Archiving and Interchange and even the Journal Publishing are very flexible models that allow content to be tagged in different ways
The DTD Spectrum
Conversion Creation
Is Journal Publishing meeting our needs?
Not really. It is too restrictive for some users, and not prescriptive enough to be a good Authoring model.
The DTD Spectrum
Conversion Creation
Article Authoring DTD
A reasonable question• (1) It seems from the element reference page for <chem-struct-wrap> that one could
omit explicit labels because "A <chem-struct-wrap> may also be numbered, automatically by a formatting application or by preserving the number inside a <label> element." Having seen this, but not found similar comments about "automatic numbering" for other elements that may typically be numbered/labelled, I would like to know what the assumption is about omitting labels in general for these (e.g. chemical structures, equations, figures, tables, etc.): is a formatting application expected by default to generate a number/label? If so, is there a way to suppress numbering for some occurrences?
• (2) Relatedly, what is the expected behaviour for an <xref> element that has no content (e.g. one that (a) references an element for which automatic numbering has been assumed and which therefore lacks a <label>, or (b) one that references an element possessing a <label>)?
• Message from Simon Newton to [email protected] on September 7, 2011
A reasonable question• (1) It seems from the element reference page for <chem-struct-wrap> that one could
omit explicit labels because "A <chem-struct-wrap> may also be numbered, automatically by a formatting application or by preserving the number inside a <label> element." Having seen this, but not found similar comments about "automatic numbering" for other elements that may typically be numbered/labelled, I would like to know what the assumption is about omitting labels in general for these (e.g. chemical structures, equations, figures, tables, etc.): is a formatting application expected by default to generate a number/label? If so, is there a way to suppress numbering for some occurrences?
• (2) Relatedly, what is the expected behaviour for an <xref> element that has no content (e.g. one that (a) references an element for which automatic numbering has been assumed and which therefore lacks a <label>, or (b) one that references an element possessing a <label>)?
• Message from Simon Newton to [email protected] on September 7, 2011
A reasonable question• (1) It seems from the element reference page for <chem-struct-wrap> that one could
omit explicit labels because "A <chem-struct-wrap> may also be numbered, automatically by a formatting application or by preserving the number inside a <label> element." Having seen this, but not found similar comments about "automatic numbering" for other elements that may typically be numbered/labelled, I would like to know what the assumption is about omitting labels in general for these (e.g. chemical structures, equations, figures, tables, etc.): is a formatting application expected by default to generate a number/label? If so, is there a way to suppress numbering for some occurrences?
• (2) Relatedly, what is the expected behaviour for an <xref> element that has no content (e.g. one that (a) references an element for which automatic numbering has been assumed and which therefore lacks a <label>, or (b) one that references an element possessing a <label>)?
• Message from Simon Newton to [email protected] on September 7, 2011
• Simon is asking for “Best Practices”
• So I was thrilled to see the following response:
I don't think any assumptions are made regarding when and exactly how numbering should be automated; there is only a recognition that it commonly done in publishing systems, and JATS is designed to support this (or no numbering at all) or not, depending on local policies.
Neither is there any expectation that by default, a formatting application will number things.
This means you have both the opportunity and the burden to define a policy that makes the most sense for your data and workflow.
Message from Weldell Piez to [email protected] on September 8, 2011
I don't think any assumptions are made regarding when and exactly how numbering should be automated; there is only a recognition that it commonly done in publishing systems, and JATS is designed to support this (or no numbering at all) or not, depending on local policies.
Neither is there any expectation that by default, a formatting application will number things.
This means you have both the opportunity and the burden to define a policy that makes the most sense for your data and workflow.
Message from Weldell Piez to [email protected] on September 8, 2011
Best Practices must be scoped
• They must make sense with your content.… with your workflow… and for any users of your content down
the line.
A “quick” question
Question on usage sent in an email earlier this week from a large medical journal on "how the NLM uses the JATS Tags":
“We have just a quick question for NLM: Do you use the article-type attribute values? If we were to use our own attribute [value]s, would that pose problems for aggregators?”
Parse the question
What are the Best Practices for @article-type values?
Will it give our users problems if we just made something up?
I had to answer from 2 points of view:
Factual content about the @article-type attribute:
The @article-type attribute was a controlled list of values in the Journal Publishing model until we moved to version 3.0 at the end of 2008, which should give you an idea of how important the NLM DTD Working Group thought that that attribute is.
More facts
The one thing I would like to remind you is that the @article-type attribute is really for identifying the article type to your processors – it is not "Content". The area we've designed to display the article headings (like TOC headings for example) is the <article-categories> element with the <subj-group> structure inside.
More facts
So, for example. If you have three journals and each one displayed corrections with a different heading, you could use @article-type="correction" in all of the files so that your processing systems wouldn't need to know that you make this distinction. But then you could have one journal that uses <subject>Correction</subject>, and two that use <subject>Erratum</subject>.
And then my opinion about how the article-type should be used (based on what we do in PMC) from the point of view of Aggregators.
The short best answer is that you probably need to speak with your aggregators about the values that you will be using and they will be accepting. Aggregators are going to want to normalize the list of article types so that they don't have to process many different values that mean the same thing in their system. This can happen in two ways.
The easiest way for the aggregator is for them to give you a set of values to use and anything outside of that set is not accepted. The way that a lot of aggregators work is that they normalize these values on the way in to their preferred set. But this means you will need to have a conversation with them to map your values to their values. In reality at PMC, we see things a little of both ways.
We have the PMC Tagging Guidelines (http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/style.html) – which is essentially a "Best Practices" for tagging articles in NLM XML for submission to PMC. We have a list of @article-type attribute values there that we will accept. If we find something outside of this set in a submission that can obviously map to one of our values, we will normalize it on ingest. For example, we use @article-type="correction" in PMC.
When we get a submission with @article-type="erratum" or @article-type="errata", we convert it to @article-type="correction". But if we get a submission with @article-type="expression-of-embarassment" or @aricle-type="do-over", we will contact the submitter to be sure we have the mapping right.
Essentially - If you were sending this to PMC, this is what we would do. OR "Your data in MY workflow can be handled in these ways".
The “Best Practices” are related to the project.
• Which is just restating Wendell's position. She has both the burden and the opportunity to define a policy that makes sense for her data and her workflow.
• So, Best Practices are great - within the scope of a project.
Time to get on with the conference.
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