# Archiving and Interchange Tagset Working Group Meeting

18 August, 2003

NLM Board of Regents Room

National Library of Medicine

## Attendees

### Archiving and Interchange Tagset Working Group {#archiving-and-interchange-tagset-working-group .Bullet-Head}

-   Adriana Ardeleanu (Microsoft)

-   Matthew Cockerill (BioMed Central)

-   Mark Doyle (American Physical Society)

-   Beth Friedman (Data Conversion Laboratories, Inc.)

-   Gerry Grenier (IEEE)

-   

-   Evan Owens (JSTOR Electronic Archiving Initiative)

-   Diana Robinson (HighWire Press)

-   Nick Twyman (Public Library of Science)

-   Tommie Usdin (Mulberry Technologies, Inc.)

-   Roy Williams (Cal Tech)

### NCBI {#ncbi .Bullet-Head}

-   Jeff Beck

-   Laura Kelly

-   Sergey Krasnov

-   David Lipman

-   Jim Ostell

-   Ed Sequeira

### Archiving and Interchange DTD Secretariat {#archiving-and-interchange-dtd-secretariat .Bullet-Head}

-   Deborah Lapeyre (Mulberry Technologies, Inc.)

## 1.0 Agenda (distributed at the meeting)

1.  Call to Order and Opening Remarks\
    housekeeping details

2.  Discussion of Scope for Working Group

3.  

4.  Open Discussion on Suggested Additions/Changes to Tagset

5.  Review of Notable Suggestions Made by Users

6.  Summary Of Conclusions And Identification Of Areas For Discussion

7.  Closing remarks

    NOTE: There will be no confidential information discussed at the
    Archiving and Interchange Tagset Working Group meeting.

## 2.0 Administrative Material

### 2.1 Scope of the Working Group

The Archiving and Interchange Tagset Working Group has been established
to provide NCBI with industry feedback concerning the Archiving and
Interchange DTD Suite as well as tools and utilities to store, retrieve,
convert, display, and archive data tagged according to this suite. The
hope is that, with guidance from the Working Group, the Suite and
related products can be made useful, not only to NCBI, but to the larger
electronic publishing and archiving communities.

### 2.2 Working Group Meetings

Subsequent meetings of the Working Group will take place as conference
calls, with much of the work accomplished through email discussions. The
first remote meeting of this Working Group will be during the week of
November 3-7, 2003, not to be held on US election day. The numbers for
the conference call and agenda will be distributed in advance. The date
will be chosen soon and emailed to all participants.

### 2.4 Discussion Groups Established During the Meeting

### Authoring Tool Discussion Group

-   Adriana Ardeleanu

-   Matthew Cockerill

-   Mark Doyle

-   Nick Twyman

-   Jeff Beck (to take lead in forming group)

### Discussion Group for External XML Structures

-   Jim Ostell

-   

-   Mathew Cockerill

-   Nick Twyman

-   (Public Library of Science)

-   Tommie Usdin

-   Roy Williams

-   Jeff Beck (to take lead in forming group)

## 3.0 Issues Discussed

-   The scope, purpose, and relationships among the Archiving and
    Interchange DTD (hereafter Green DTD), the Publishing DTD (hereafter
    the Blue DTD), and the original and revised original PMC DTDs.

-   What went wrong with ISO 12083 and how not to have this DTD suffer
    the same fate

-   How to avoid the negative baggage that NLM projects sometimes arouse
    in the publishing community.

-   What tools should be developed to enable use and facilitate adoption

-   The process by which additions, corrections, and tools should be
    considered and implemented.

-   The specific list of Tagset and DTD Suite changes brought to the
    meeting by the Archiving and Interchange Secretariat. These
    suggestions came from the open discussion list and from the "Phase
    II" comments in the original DTD.

-   What is necessary to get this group to consider a
    modification/addition to the Tagset?

-   How does the DTD Suite handle "Islands" of foreign tagging, such as
    CML or other valid (to some DTD or schema) XML Tagset?

-   Print version of the Tag Library

## 4.0 Recommendations

### 4.1 Develop and Promote DTD Tools and Utilities

The world at large will not adopt a DTD suite, however meritorious,
unless there is ample tool support. Therefore, to increase adoption,
NCBI should develop, solicit, promote, and make centrally available
tools to work with this suite and links to such tools on other sites.

Existing and already planned tools include:

-   Preview/Converter (XML by Green DTD to HTML)

-   Preview/Converter (XML by Blue DTD to HTML)

-   Converter( XML by pmc-1 DTD to Green DTD)

-   Converter (DocBook XML to Green DTD)

-   Other Converters (from XML according to a few of the widely used
    Publisher DTDs such as Keton and HighWire)

-   Print (Blue instance to PDF)

-   W3C XML Schema version of Blue DTD

    Other Tools Suggested by the Working Group

-   Authoring tool for Microsoft Word

-   Online Validator to check Blue and Green instances

-   Additional converters from major publishing DTDs

### 4.2 User Contribution Area

-   Need an area of the website where individuals and organizations may
    contribute tools such as stylesheets, authoring customization
    packages, and converters.

-   NCBI should establish a tool catalog with descriptions of tools and
    URIs (partly a list of links, partly an archive for downloading)

-   Authors of such products will be encouraged to put their source into
    SourceForge (or other open access mechanism) and provide a
    description, metadata, and links to NCBI for the tool catalog

### 4.3 Open Change Process

-   The Working Group should include one or more members from active,
    traditional scientific and medical publishers.

-   Suggestion for changes, additions to the tagset will continue to be
    taken from the open, public list.

-   Changes (except error corrections) should be undertaken on a regular
    basis (quarterly, twice-annually, and annually were mentioned)

-   The Working Group will vet suggestions and set priorities.

-   A mechanism should be established to let users, easily and in one
    place, review current issues under consideration.

## 5.0 Further Discussion Needed

There were several semantic tagging or enhanced structural tagging
suggestions where the Working Group felt that further information was
needed. Any parties who desire the following changes should present use
cases and scenarios, tagging utility or rationales, and a description of
any structural-only alternative to the tagset proposed. How is the
equivalent structure being handled by DTDs and schemas now?

Such unresolved issues include:

-   Questions and Answers (in the formal sense)

-   Taxonomic Key

-   SVG

-   Island of foreignly-tagged material within the Green XML stream

## 6.0 Out of Scope

Potential additions to the Tagset that the Working Group felt were out
of scope for this group:

-   Packaging or delivery wrapper standards;

-   Digital rights management (rights metadata and acceptable usage
    metadata should be in another layer and not part of the DTD Suite);

-   Metadata complete enough for content harvesting;

-   Forms and fill-in-the-blank formatting tagging; and

-   Non-article material such as: ads, job ads, classified advertising,
    display advertising; calendars, meeting schedules, and
    announcements; and journal material such as author guidelines,
    policy and scope statements, editorial and advisory boards, and
    detailed indicia, except as such material could be translated into
    ordinary paragraphs, lists, sections, etc.

# Appendix A. Detailed Tagset Suggestions

### A.1 How to Submit Tagset Addition Requests

The following informal change process was recommended until NCBI writes
more formal procedures. Error reporting should be on the list or by
email, as succinctly as possible. For additional structural or new
semantic material, a petitioner should provide at least the following:

-   Rationale for change; assertion of benefit;

-   Description of need and community;

-   Coded examples; and

-   If appropriate, display examples in a readily read format like HTML
    or PDF.

### A.2 Element/Structure Changes and Additions

-   **Tables**---#1)Add the CALS DTD fragment to the Green DTD #2) Add
    the CALS fragment to the Blue DTD and restrict the Green DTD to
    whatever the PubMed Central archive wants

-   **Alternative versions**---Allow more than one version of tables,
    graphics, etc. e.g, a table and a gif for a tabular structure;
    MathML , TeX, gif combination for an equation, etc.

-   **Media Object**---yes, give us a tag for it, either by adding a new
    \<media\> element (or equivalent) or be redefining what a
    \<graphic\> is.

-   **Named content**---expand its content model to allow more inside it

-   **Labels**---in Green, allow them on almost anything, but treat this
    as an override and document it as such

-   **URL in DTD**---Consider at least a list of the most recent URLs
    where the material could be found, or point to the top level

-   **Full journal title**---Add an element in the metadata

### A.3 Attribute Additions and Changes

-   Add a "type" attribute or equivalent to \<target\>

-   Add an "ID" attribute or equivalent to \<paragraph\>

-   Add the ability to say that a footnote concerns Conflict of Interest

-   Add an "information-class" and/or "role" attribute or equivalent to
    (at least) \<paragraph\> and consider it for most large structures
    such as def lists, sections, etc. For green this is CDATA, for other
    this may be an explicit list with an "other" escape hatch and CDATA
    attribute for recoding the other.

### A.4 Consider Incorporation of Other Standards

-   OAI (Open Archives Initiative Protocol for Metadata Harvesting)

### A.5 Postponed for Now

-   XLink extended links

# Appendix B. Suggestions for DTD and Documentation Changes

This list was provided to the attendees at the meeting. Some of the
items were discussed briefly, if at all. All conclusions and
recommendations from those discussions are listed in the minutes.

# Suggestions for DTD & Documentation Changes

### August 2003

These comments and suggestions have been collected from comments made on
the DTD discussion lists and email from people working with the DTDs.

## Category: FAQ 

Change which? **Both** Change what? **Documentation**

Request No: **17**\
Requestor: **Nick Twyman** \<ntwyman@plos.org\>

I was hoping to get a better understanding of the status of the
publishing-dtd and it\'s relationship to the existing pmc-1.dtd
document.

We\'re in the process of setting up our publishing systems and want to
make sure we are in-line with the NCBI/PMC standards right from the
start. Question is, when will NCBI start using the Journal Publishing
DTD for submissions into PMC?

I am assuming that if we adopt the Journal Publishing DTD from the start
this will not be a problem.

## Category: FAQ 

Change which? **Archiving** Change what? **Documentation**

Request No: **26**\
Requestor: **\"Hollinger, Blaine\"** \<blaineh@bcm.tmc.edu\>

Expand the description of the reason for these tag sets and the expected
uses.

### Why: 

Users who send email to the list such as:\
I have no idea what this is about and you don\'t do a good job of
telling me what benefit it is or why I should want to use it?

## Category: Major 

Change which? **Both** Change what? **Tag Set**

Request No: **5**\
Requestor: **DTD comment via BTU**

Add structures for encoding Questions and Answers. (We can currently do
this with paragraphs, but that doesn\'t capture the real content of the
Q&A pairs.)

### Why: 

This would be useful in instructional material and interviews. Also in
CME materials (see suggestion on CME)

## Category: Major 

Change which? **Both** Change what? **Tag Set**

Request No: **6**\
Requestor: **DTD comment via BTU**

Add structures for Continuing Medical Education materials

### Why: 

These materials are sometimes included in journals. At present they can
be encoded as paragraphs, but that is not a satisfactory way to capture
the true intent of the material.

## Category: Major 

Change which? **Both** Change what? **Tag Set**

Request No: **7**\
Requestor: **DTD comment via BTU**

Forms and fill-in-the-blank material. We could add structures for
capturing the content of forms, including the blanks to fill in, etc.

### Why: 

These materials are sometimes included in journals. At present they can
be captures as graphics, which are not generally searchable.

## Category: Major 

Change which? **Both** Change what? **Tag Set**

Request No: **10**\
Requestor: **Original DTD comment**

Advertising included in the journal. This may include: job ads,
classified advertising, display advertising.

### Why: 

Some readers may feel that the advertising included in the journal is as
interesting as the article content. We currently have no way to capture
anything in addition to article content from journals.

## Category: Major 

Change which? **Both** Change what? **Tag Set**

Request No: **11**\
Requestor: **Original DTD comment**

Calendars, meeting schedules, and announcements.

### Why: 

These can be handled as articles, but the difference in type of material
may be important to some users.

## Category: Major 

Change which? **Both** Change what? **Tag Set**

Request No: **12**\
Requestor: **Original DTD comment**

Add structures to preserve about the journal materials, including author
guidelines, policy and scope statements, editorial and advisory boards,
detailed indicia, etc.

### Why: 

These can be handled as articles, but the difference in type of material
may be important to some users.

## Category: Major 

Change which? **Archiving** Change what? **Tag Set**

Request No: **19**\
Requestor: **Wendell Piez**

Consider an information class (\"class\" or \"type\" perhaps) attribute
on most generic structures: paragraph, sec, speech, stmt, def-list, etc.
for capturing more specific tagging in source documents.

Request No: **43**\
Requestor: **Wendell Piez**

Elsevier also adds a \"role\" attribute to the \<p\> element. This is
documented as \"The attribute role allows one to categorize paragraphs,
and attach a special meaning to them. For instance, it makes it possible
to mark a paragraph as a \"motto\", and handle it in a different way
than an ordinary paragraph.\" This would essentially be like the HTML
class attribute in that it gives an additional back door to semantically
qualify domain-specific material without adding new elements.

## Category: Major 

Change which? **Archiving** Change what? **Tag Set**

Request No: **36**\
Requestor: **Bruce D. Rosenblum** bruce@inera.com

add structures for Taxonomic Keys

For the moment, it looks like it\'s best to handle with head-less
sections, named-content, and list-content. However I would like to
request that the review board consider adding a taxonomic model to the
DTD at some point in the near future to accommodate the needs of the
bioone DTD along with several other publishers that have this
requirement.

named-content is working really well for us, too. We have directed
several DTD users towards it with very nice results. We also have a
group that\'s using the list-content attribute for a taxonomic key
section! It was exactly what they needed to avoid a set of new elements.

## Category: Major 

Change which? **Archiving** Change what? **Tag Set**

Request No: **37**\
Requestor: **Bruce D. Rosenblum** bruce@inera.com

handle borders on table cells.

Much to my dismay, I just discovered that XTHML has NO table cell
borders. How are we supposed to put lines under table headers, or under
individual cells in table headers. Please let me know if I\'m missing
something, since I suspect this will cause significant problems when
converting many CALS tables to the NLM DTD.

## Category: Major 

Change which? **Both** Change what? **Documentation**

Request No: **48**\
Requestor: **DAL**

Beef up the examples. Provide at least one rich example of each element.
For many that can be used in several ways, provide examples of several
contexts in which the element can be used.

## Category: Minor 

Change which? **Both** Change what? **Tag Set**

Request No: **1**\
Requestor: **Jeff Beck** hammerhead@nih.gov 301-435-5992

We need to be able to allow an \"alternate version\" for
\<display-formula\> and \<inline-formula\> or at least allow for
multiple encodings or representations of the same piece of math.

### Why: 

We need to be able to allow an \"alternate version\" for
\<display-formula\> and \<inline-formula\>. or at least allow for
multiple encodings or representations of the same piece of math.

## Category: Minor 

Change which? **Both** Change what? **Tag Set**

Request No: **2**\
Requestor: **Jeff Beck** hammerhead@nih.gov 301-435-5992

need to add a way to tag that an article is \"open access\" not just
leave off the copyright line

Request No: **9**\
Requestor: **Jeff Beck** hammerhead@nih.gov 301-435-5992

Electronic and digital rights management information

## Category: Minor 

Change which? **Archiving** Change what? **Tag Set**

Request No: **3**\
Requestor: **Jeff Beck** hammerhead@nih.gov 301-435-5992

We need to allow movies as a display object (like figures) and not just
as supplemental data.

## Category: Minor 

Change which? **Both** Change what? **Tag Set**

Request No: **8**\
Requestor: **DTD comment via BTU**

Conflict of interest statements and financial disclosures.

### Why: 

This content is now encoded as paragraphs, generally in a footnote.
Since this content is important to many readers it might be useful to
specifically identify it.

### Example: 

\<ack\>\<p\>The meeting was sponsored by the Medical Research Council,
UK, with financial support from the Wellcome Trust, and Carl Zeiss Ltd.
We thank Jim Duffy for drawing \<figr rid=\"f2\"\>Fig. 2\</figr\>, and
the meeting\'s speakers for agreeing to the included citations. S.M.G.
is supported by the Swiss National Science Foundation and D.L.S. by the
National Institute of General Medical Sciences/NIH, USA.\</p\>\</ack\>

\<ack\>\<p\>This work was supported by the Imperial Cancer Research Fund
and the Human Frontiers Science Program. A.C. was supported by a
European Science Exchange Fellowship from the Royal Society and the
Swiss National Foundation, M.T. was supported by an EMBO Fellowship and
J.K.K. is a Boehringer Ingelheim Fonds scholar.\</p\>\</ack\>

## Category: Minor 

Change which? **Both** Change what? **Tag Set**

Request No: **13**\
Requestor: **BTU**

Add a place to store the full journal title. We can currently capture a
wide variety of journal title abbreviations, but not the full title.

### Example: 

\<title type=\"journal\"\>Epilepsy Currents\</title\>\
\<title type=\"journal\"\>Neurology\</title\>

## Category: Minor 

Change which? **Both** Change what? **Tag Set**

Request No: **14**\
Requestor: **B Rosenblum** \<bruce@inera.com\>

Add extended links to xlink. I just took a look at common.ent and
noticed that in both cases, xlink:type is fixed as \"simple\". Did you
chose to avoid extended linking because, in reality, no one\'s really
doing it yet? Any comments on the topic, or the specific questions
raised above would be appreciated.

### Why: 

Debbie noted: Yep, all we gave them was HTML href-style links. IF
anybody is actually doing extended multi-headed links in journal
publishing, that can be one of the first things they ask the advisory
board for, I\'ll believe it when I see it.

I have seen good use of out-of-line linking, but not in STM journal
publishing and not in the kind of material that Pub Med Central and
Harvard/Mellon/Yale are archiving, even in the book material.

Tell them that, putting something into the DTD is an implicit promise
that it will exist, and therefore a burden on every implementor. We did
not go with fancy linking, by design, to cut the implementation and
conversion burden, UNTIL SUCH TIME AS IT PROVES USEFUL.

## Category: Minor 

Change which? **Both** Change what? **Documentation**

Request No: **15**\
Requestor: **B Rosenblum** \<bruce@inera.com\>

In the link.ent section, use of XLink global attributes is mentioned. I
would appreciate clarification on the scope of the XLink functionality.
Useful features of XLink are extended linking and out-of-line linking.
If possible, could you please provide further explanation or example of
how this might work in practice.

## Category: Minor 

Change which? **Archiving** Change what? **Tag Set**

Request No: **18**\
Requestor: **Wendell Piez** wapeiz@mulberrytech.com

Named-content was envisioned as an inline, phrase-level object. As such,
it should contain at least the %inline-display.class inline-graphic
private-char and probably the %simple-intable-display.class as well as
chem-struct, graphic, and preformat

But there is also the question of whether named content should be a
larger structure, allowed to contain anything a paragraph could contain.

### Why: 

We actually wanted to put a graphic in a named-structure.

## Category: Minor 

Change which? **Archiving** Change what? **Tag Set**

Request No: **20**\
Requestor: **Wendell Piez**

Consider adding non-hierarchical heading at the paragraph level.

### Why: 

Capture headings that are not part of the structure of the article, such
as in Nature.

## Category: Minor 

Change which? **Archiving** Change what? **Tag Set**

Request No: **22**\
Requestor: **B Rosenblum** bruce@inera.com

Add \<no\> to a whole lot of elements. While we\'re cross-checking,
Elsevier has the \<no\> element (their equivalent of \<label\>) in the
following places:\
\<cor\>\
\<aff\>\
\<sec\>\*\
\<bib\>\*\
\<bb\>\*\
\<other-ref\>\*\
\<app\>\*\
\<fn\> (did I really leave it at the symbol attribute here?)\
\<enun\>\* (our \<statement\>)\
\<l\>\
\<dl\>\
\<list\>\*\
\<list-item\> (I think we agreed to forego it here)\
\<tbl\>\*\
\<tblfn\>\
\<fig\>\*\
\<textbox\>\
\<upi\>\
\<fd\>\
On a quick look, I think we got the ones with the \*, but it looks like
we may have missed a bunch of others

### Why: 

People converting content from Elsevier journals.

## Category: Minor 

Change which? **Archiving** Change what? **Documentation**

Request No: **29**\
Requestor: **Robert C. Leif** \<rleif@rleif.com\>

By the way all DTDs, Schema, and other XML documents that can be
downloaded should include the URL from whence they came. The W3C even
includes the URL of the latest version.

## Category: Minor 

Change which? **Archiving** Change what? **Tag Set**

Request No: **34**\
Requestor: **Bruce D. Rosenblum** bruce@inera.com

Now that we\'re going into production with the DTD for one of our
customers, we keep running into little things. Today I noticed that
somehow we didn\'t add \<label\> to \<list-item\>. Can you please add
this to the errata list. It\'s essential to correctly handle University
of Chicago and Elsevier 5.0.

Request No: **21**\
Requestor: **Bruce D. Rosenblum** bruce@inera.com

I just was setting something up and noticed we don\'t have \<label\> in
\<aff\>.

We need it to replicate the Elsevier model of:\
\
\<!ELEMENT aff - o ( no?, %data;, %cty-cny; )\>\
\<!ATTLIST aff\
id ID #IMPLIED\>

Request No: **41**\
Requestor: **Bruce D. Rosenblum** bruce@inera.com

In addition to the \<p\> changes I sent earlier today, \<aff\> needs
\<label\>, and actually so does \<corresp\> (see Elsevier DTD 4.3 and
5.0 - in 4.3 and later, their QCTool requires \<label\> in a cor). I
think you talked me out of label in corresp before by arguing that
footnote could be used instead, but for ease of conversion we really do
need it. I\'m more than happy to have you bury it in a parameter entity
so you can easily remove it from publishing DTDs :)

## Category: Minor 

Change which? **Archiving** Change what? **Tag Set**

Request No: **40**\
Requestor: **Wendell Piez**

Remove \<attribution\> from \<verse-group\> as it is a) susceptible to
tag abuse and b) semantically incorrect modeling.

The attribution is part of the larger unit (such as a display-quote) (or
epigraph if we had them) that should be able to contain a title,
verse-group, attr, etc. Display quote has such a model.

So, either add \<poem\> or other wrapper or delete \<attribution\> from
versegroup.

Request No: **45**\
Requestor: **Wendell Piez**

Describe/demonstrate how to encode the attribution of verse.

### Why: 

People who won\'t know how to use the DTD in this case.

## Category: Minor 

Change which? **Archiving** Change what? **Tag Set**

Request No: **42**\
Requestor: **Bruce D. Rosenblum** bruce@inera.com

We should add an ID attribute to \<p\>. I\'m starting to see DTDs (e.g.
Elsevier 5.0) in which this is being done so that linkages can be made
to arbitrary paragraphs.

## Category: New Service or Facility 

Change which? **Archiving** Change what? **Documentation**

Request No: **23**\
Requestor: **David Holden** \<dh@iucr.org\>

Do you have a printable version of your archive-dtd documentation?

## Category: New Service or Facility 

Change which? **Archiving** Change what? **Tag Set**

Request No: **24**\
Requestor: **Robert C. Leif** \<rleif@rleif.com\>

Please translate your DTDs into XML schemas. XMLSpy can be used for this
purpose.

### Why: 

The schemas will then work with Microsoft Word 2003 and other modern
software.

## Category: New Service or Facility 

Change which? **Archiving** Change what? **Tag Set**

Request No: **27**\
Requestor: **Alain Boisvert**

publish stylesheets to use with the DTD.

I would like to use this DTD but we need XSL style sheets to publish

Are there already developed style sheets?