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

On Mon, Apr 8, 2013 at 2:20 AM, Maori Ito <maori@nibio.go.jp> wrote:

> 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?
>

the idea is to broaden from species of origin to the specific system that
contains or produces the entity (gene, chemical, protein, lipid, etc). For
instance, consider a chemical was produced by a genetically engineered
microbial species. While it would not appear in the list of species in the
NCBI taxonomy, it might appear in a catalogue/ontology of cell types or
cell lines. Similarly, a protein may have been produced in an in vitro
system, but we should be able to express this relationship to that
production system.


> 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<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<http://wiki.lifesciencedb.jp/mw/index.php/BH12.12/schema.org#ex1.29_KEGG_DISEASE>



i see. yes, it's nice to include links to other resources to create that
linked data effect. Perhaps we could make it "see other" or "related
entry"? That would help indicate that another database entry is being
referenced.


>
>
>  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<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
>
>
good job!  let us know your progress and feel free to ask for more feedback
on a revised proposal.

m.


>
> --
> -- :-);-)
> 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<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<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=
>> **dW5ndHMzNmg2NW81MnFxY2IxYWxsc2**hlNThfMjAxMzA0MDJUMTUwMDAwWiBw**
>> dWJsaWMtc2Vtd2ViLWxpZmVzY2lAdz**Mub3Jn&tok=**
>> MTcjdzMuaGNsc0BnbWFpbC5jb21iY2**Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZk**
>> NzQ3OGRjZWY2NjU1Mzc5&ctz=**America/New_York&hl=en<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.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<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<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<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://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<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<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=**dW5ndHMzNmg2NW81MnFxY2IxYWxsc2**hlNThfMjAxMzA0MDJUMTUwMDAwWiBw**
>> dWJsaWMtc2Vtd2ViLWxpZmVzY2lAdz**Mub3Jn&rst=1&tok=**
>> MTcjdzMuaGNsc0BnbWFpbC5jb21iY2**Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZk**
>> NzQ3OGRjZWY2NjU1Mzc5&ctz=**America/New_York&hl=en<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=**
>> dW5ndHMzNmg2NW81MnFxY2IxYWxsc2**hlNThfMjAxMzA0MDJUMTUwMDAwWiBw**
>> dWJsaWMtc2Vtd2ViLWxpZmVzY2lAdz**Mub3Jn&rst=3&tok=**
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>> NzQ3OGRjZWY2NjU1Mzc5&ctz=**America/New_York&hl=en<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=**
>> dW5ndHMzNmg2NW81MnFxY2IxYWxsc2**hlNThfMjAxMzA0MDJUMTUwMDAwWiBw**
>> dWJsaWMtc2Vtd2ViLWxpZmVzY2lAdz**Mub3Jn&rst=2&tok=**
>> MTcjdzMuaGNsc0BnbWFpbC5jb21iY2**Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZk**
>> NzQ3OGRjZWY2NjU1Mzc5&ctz=**America/New_York&hl=en<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=**dW5ndHMzNmg2NW81MnFxY2IxYWxsc2**
>> hlNThfMjAxMzA0MDJUMTUwMDAwWiBw**dWJsaWMtc2Vtd2ViLWxpZmVzY2lAdz**
>> Mub3Jn&tok=**MTcjdzMuaGNsc0BnbWFpbC5jb21iY2**
>> Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZk**NzQ3OGRjZWY2NjU1Mzc5&ctz=**
>> America/New_York&hl=en<https://www.google.com/calendar/event?action=VIEW&eid=dW5ndHMzNmg2NW81MnFxY2IxYWxsc2hlNThfMjAxMzA0MDJUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21iY2Y2NWMyMTE2NDkwZmY5MTk3YWMzMTZkNzQ3OGRjZWY2NjU1Mzc5&ctz=America/New_York&hl=en>
>> >
>>
>> Invitation from Google Calendar <https://www.google.com/**calendar/<https://www.google.com/calendar/>
>> >
>>
>> You are receiving this courtesy email at the account
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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
>
>
>


-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com