Re: Updated Invitation: HCLS - all @ Tue 2013-04-02 10:00 - 11:00

Hello, I'm Maori @ Osaka.
Thank you for listening my presentation and mail.
I'm sorry my reply is late.
(I confused Biohackathon ML and I didn't join this ML before.
Besides, my English is not so good. Sorry in advance if I'm wrong.)

I'm appreciate your suggestions and comments.
I discussed them with our project members.

>1. allow/enforce the reference to be a URL, such as the pubmed entry or a doi

We agree this suggestion. It's not always true that all of papers have ID.
I'd like to think about how to mark up with URL is suitable.

>2. allow the taxon to be also be a URL.

Mark-up candidate for taxon have already could written with URL.
Taxon uses a nest with biological database entry to mark-up, so we can also use
all of other kinds of properties (in BiologicalDatabaseEntry) including URL.

>Perhaps broaden this to "biological-source", so that we could use types from the cell type ontology
or the cell line ontology, or specify some species-specific anatomy.

Sorry I couldn't understand the meanings.
Do you want to use other ontology in taxon?
If you want to other vocabularies or properties which are not proposed in schema.org,
we have to think about its vocabularies. If you need other vocabularies, we'd like to
think about lower class of BiologicalDatabaseEntry with specialist.
But I'd like to avoid complication to increase applied database.

>3. what's the meaning of seeAlso?
The meaning of seeAlso is reference URL.
Basically, it is based on "relatedLink" in "WebPage".
http://schema.org/WebPage
However relatedLink can only use URL, we thought it had better to use other properties, therefore
we proposed seeAlso which can use other properties in BiologicalDatabaseEntry which is based on rdfs.
http://www.w3.org/TR/rdf-schema/#ch_seealso

(Results Image <KEGG DISEASE> seeAlso is shown under the snippet.)
http://wiki.lifesciencedb.jp/mw/index.php/BH12.12/schema.org#ex1.29_KEGG_DISEASE

>there was also some discussion about the relationship of rdfa and schema.org of microdata.

I think it is enough you can do one of two things.
Our main goal is to show the search results richer.
We applied microdata because major search engines decided to use mainly.
http://support.google.com/webmasters/bin/answer.py?hl=en&answer=1211158
Ref.Why microdata? Why not RDFa or microformats?

However, the important part is to attach a meaning which can be understood by Computer.
Indeed, google also support RDFa.
In case of sagace, I'd like to consider making RDFa crawler in addition to microdata crawler.

If you have any suggestions or comments (and mistakes;;), please let me know:-)

Maori


-- 
-- :-);-)
Maori Ito
Email : maori@nibio.go.jp
National Institute of Biomedical Innovation (NIBIO)
Bioinformatics Project : http://mizuguchilab.org/
Sagace : http://sagace.nibio.go.jp


Hi,
  Maori's slides are available here:
http://www.w3.org/wiki/images/6/6f/2013-hcls-maori-ito-db-schema-dot-org.pdf

  Given the proposal:
http://www.w3.org/wiki/WebSchemas/BioDatabases#BiologicalDatabaseEntry

major suggestions included
1. allow/enforce the reference to be a URL, such as the pubmed entry or a
doi
2. allow the taxon to be also be a URL. Perhaps broaden this to
"biological-source", so that we could use types from the cell type ontology
or the cell line ontology, or specify some species-specific anatomy.
3. what's the meaning of seeAlso?

there was also some discussion about the relationship of rdfa and
schema.orgmicrodata... i don't think it was clear to those
participating whether
developers should include both or just one? or if there is a way to get
both from one + automatic translation?

Cheers,

m.



On Sat, Mar 30, 2013 at 10:46 AM, Health Care Life Sciences <
w3.hcls@gmail.com> wrote:

> This event has been changed.
> more details »<https://www.google.com/calendar/event?action=VIEW&eid=dW5ndHMzNmg2NW81MnFxY2IxYWxsc2hlNThfMjAxMzA0MDJUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21iY2Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZkNzQ3OGRjZWY2NjU1Mzc5&ctz=America/New_York&hl=en>
> HCLS - all
> *Changed: *Please join us this week (note - 10am EDT!) to hear from Maori
> Ito on schema.org extensions for biomedical databases, with an
> opportunity to discuss these in depth.
>
> Title: Enhanced search for life science databases with proposed schema.orgextension
> Presenter: Maori Ito, National Institute of Biomedical Innovation, Osaka
>
> Abstract: Lack of unified annotation makes it difficult to find specific
> information across a set of life science databases. Here, we discuss
> proposed extensions to schema.org to semantically annotate biological
> databases and their entries using the microdata format. We have applied
> this to Japanase biomedical data & resources to provide additional fields
> in our search results. We hope to finalize this proposal and encourage
> databases to adopt the extension, thereby improving the quality of search
> results.
>
> W3C Wiki page :
> http://www.w3.org/wiki/WebSchemas/BioDatabases#BiologicalDatabaseEntry<http://www.google.com/url?q=http%3A%2F%2Fwww.w3.org%2Fwiki%2FWebSchemas%2FBioDatabases%23BiologicalDatabaseEntry&usd=2&usg=AFQjCNHXuP3y8aHzXCH_zjKze4NZ6rRelQ>
> Properties and example of markup are shown in this page.
>
> BioHackathon2012 : https://github.com/dbcls/bh12/wiki/Schema.org-extension<http://www.google.com/url?q=https%3A%2F%2Fgithub.com%2Fdbcls%2Fbh12%2Fwiki%2FSchema.org-extension&usd=2&usg=AFQjCNG-wJuEQiqM-bzotbN7s6Alve2fLA>
> How and why, discussions and useful links are shown in this link.
>
> BH12.12 (Japanese) :
> http://wiki.lifesciencedb.jp/mw/index.php/BH12.12/schema.org<http://www.google.com/url?q=http%3A%2F%2Fwiki.lifesciencedb.jp%2Fmw%2Findex.php%2FBH12.12%2Fschema.org&usd=2&usg=AFQjCNGuqF7uiMTj1LCC_Ljxcn9m5yIuow>Concrete examples of markup and search results, discussions and comments
> are shown in this link.
>
> --------------
> Meeting URL
> http://fuze.me/19277427<http://www.google.com/url?q=http%3A%2F%2Ffuze.me%2F19277427&usd=2&usg=AFQjCNHyXVGgHYPEp5M2eW0S9-k4OHdoLA>
>
> Toll / Intl #: +1 (646) 583-7415
> Toll free #:
> Attendee PIN #: 47479369
> --------------
>
> *When*
> *Changed: *********Tue 2013-04-02 10:00 – 11:00 Eastern Time
> *Calendar*
> public-semweb-lifesci@w3.org
> *Who*
> •
> w3.hcls@gmail.com - organizer
> •
> public-semweb-lifesci@w3.org
>
> Going?   ***Yes<https://www.google.com/calendar/event?action=RESPOND&eid=dW5ndHMzNmg2NW81MnFxY2IxYWxsc2hlNThfMjAxMzA0MDJUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&rst=1&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21iY2Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZkNzQ3OGRjZWY2NjU1Mzc5&ctz=America/New_York&hl=en>-
> Maybe<https://www.google.com/calendar/event?action=RESPOND&eid=dW5ndHMzNmg2NW81MnFxY2IxYWxsc2hlNThfMjAxMzA0MDJUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&rst=3&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21iY2Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZkNzQ3OGRjZWY2NjU1Mzc5&ctz=America/New_York&hl=en>-
> No<https://www.google.com/calendar/event?action=RESPOND&eid=dW5ndHMzNmg2NW81MnFxY2IxYWxsc2hlNThfMjAxMzA0MDJUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&rst=2&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21iY2Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZkNzQ3OGRjZWY2NjU1Mzc5&ctz=America/New_York&hl=en>
> *    **more options »<https://www.google.com/calendar/event?action=VIEW&eid=dW5ndHMzNmg2NW81MnFxY2IxYWxsc2hlNThfMjAxMzA0MDJUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21iY2Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZkNzQ3OGRjZWY2NjU1Mzc5&ctz=America/New_York&hl=en>
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-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

Received on Monday, 8 April 2013 08:43:59 UTC