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

Thank you for your comments. 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

Re: FDA: Semantic Web Technologies Fellowship

Great news and thanks for these links Kerstin and for this: In the last part of his talk: Talking to Machines he says "That it's odd how we share results of RCTs (Randomised, Controlled Trials) in C19th essay format!" This is also how Cochrane Collaboration share revi

Re: owl:sameAs - Harmful to provenance?

Hi Rich, On 04/08/2013 02:08 PM, Rich Cooper wrote: Dear David, You wrote: 1. Owen's URI definition will always be ambiguous. There will always exist a property p such that neither p nor its negation are entailed by the URI definition. While true, this leaves out the subjectiv

Re: owl:sameAs - Harmful to provenance?

Hi Oliver, On 04/08/2013 11:55 AM, Oliver Ruebenacker wrote: Hello David, all, What I hear you saying is primarily that: 1. It is possible to have sets of assertions such that each set is consistent, but the union is contradictory. Yes, even with all parties acting intelligently

Re: owl:sameAs - Harmful to provenance?

On Mon, Apr 8, 2013 at 2:23 PM, Alan Ruttenberg wrote: > > > > On Mon, Apr 8, 2013 at 2:10 PM, Michel Dumontier < > michel.dumont...@gmail.com> wrote: > >> >> >> >> On Mon, Apr 8, 2013 at 1:23 PM, Alan Ruttenberg > > wrote: >> >>> Nicely pointed out, TN. >>> >>> Thinking about "metadata" as some o

Re: owl:sameAs - Harmful to provenance?

On Mon, Apr 8, 2013 at 2:10 PM, Michel Dumontier wrote: > > > > On Mon, Apr 8, 2013 at 1:23 PM, Alan Ruttenberg > wrote: > >> Nicely pointed out, TN. >> >> Thinking about "metadata" as some other category of data is usually a bad >> sign. I've often found it to mean, in practice, "data I care le

Re: owl:sameAs - Harmful to provenance?

On Mon, Apr 8, 2013 at 1:23 PM, Alan Ruttenberg wrote: > Nicely pointed out, TN. > > Thinking about "metadata" as some other category of data is usually a bad > sign. I've often found it to mean, in practice, "data I care less about". > > Phil, to make the case that RDF helps here, we would want t

RE: owl:sameAs - Harmful to provenance?

hi all, phillip, not to mention a name (like mine!) is not particularly unique. cheers, michael Michael Miller Software Engineer Institute for Systems Biology > -Original Message- > From: Phillip Lord [mailto:phillip.l...@newcastle.ac.uk] > Sent: Monday, April 08, 2013 9:53 AM > To: Ol

Re: FDA: Semantic Web Technologies Fellowship

Thanks Egon and Michel - I think the current drive for clinical trial data transparency makes "getting better in talking to machines" even more important, see http://kerfors.blogspot.se/2013/03/talking-to-machines.html 2013/4/8 Egon Willighagen > On Mon, Apr 8, 2013 at 6:50 PM, Michel Dumontier

Re: owl:sameAs - Harmful to provenance?

Nicely pointed out, TN. Thinking about "metadata" as some other category of data is usually a bad sign. I've often found it to mean, in practice, "data I care less about". Phil, to make the case that RDF helps here, we would want to compare how easy it is to do significant work using the ill-repr

RE: owl:sameAs - Harmful to provenance?

Hi, - Introduction -Dublin Core: The Dublin Core Metadata Element Set is a vocabulary of fifteen properties for use in resource description. The name "Dublin" is due to its origin at a 1995 invitational workshop in Dublin, Ohio; "core" because its elements are broad and generic, usable for

Re: owl:sameAs - Harmful to provenance?

Hello Philip, Apparently, you are confusing two different cases. I talked about the same reference meaning two different things. You are talking about different references talking about the same thing. Confusion is the enemy of understanding. Take care Oliver On Mon, Apr 8, 2

Re: FDA: Semantic Web Technologies Fellowship

On Mon, Apr 8, 2013 at 6:50 PM, Michel Dumontier wrote: > Charlie, Eric, Kerstin, and others, keep up your good work to communicate > the benefits of Semantic Web technologies in simplifying and improving the > delivery of knowledge across the regulatory and pharmaceutical, clinical and > health

Re: owl:sameAs - Harmful to provenance?

And it is this bit -- "before we can do anything useful" that is utterly wrong. Recently I have spent a lot of time look at Dublin Core creator fields. You could not believe how many different ways they are used. String literals ("Phillip Lord"), last-first ("Lord, Phillip"), with abbrevs ("P. L

Re: FDA: Semantic Web Technologies Fellowship

Fantastic news! Charlie, Eric, Kerstin, and others, keep up your good work to communicate the benefits of Semantic Web technologies in simplifying and improving the delivery of knowledge across the regulatory and pharmaceutical, clinical and health care jurisdictions. Before you know it, we will

Re: owl:sameAs - Harmful to provenance?

Hello David, all, What I hear you saying is primarily that: 1. It is possible to have sets of assertions such that each set is consistent, but the union is contradictory. 2. If I don't know the meaning of these assertions, I can't prove that they are unjustified. That's pretty obvio

Re: Vocabulary

Hi Talapady, In a round about kind of way, I was asking why the gene id entries are *not* linked to their sources e.g. Which source tells us the gene id for DictyBase m. On Mon, Apr 8, 2013 at 11:21 AM, Bhat, Talapady N. wrote: > Hi, > > ** ** > > This is what I did. > > ** ** > > In t

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

On Mon, Apr 8, 2013 at 2:20 AM, Maori Ito 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.) > >

RE: Vocabulary

Hi, This is what I did. In the Web page http://xpdb.nist.gov/bioroot/bioroot.pl I typed 'Gene' and waited for it to auto fill 'Gene ID' or to show all other terms that start with 'Gene' Then I pressed enter. It gave a list of highly re-used terms with 'Gene ID' If you click on the term 'Gene I

Re: Vocabulary

We also have HGNC in Bio2RDF: p53: http://hgnc.bio2rdf.org/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fhgnc%3A11998 *HUGO Gene Nomenclature Committee [hgnc]* *Homepage:* http://www.genenames.org/ *Links:* SEARCH QUERY DOWNLOAD

Re: Vocabulary

Hi Talapady, Very interesting resource! Can you quickly explain how you generate http://xpdb.nist.gov/bioroot/bioroot.pl?allTrees=1&termid=1180437&wrd=Gene%20ID&foundin=::50:: from the sources you list here: http://xpdb.nist.gov/bioroot/help_docs/source.htm Thanks! m. On Mon, Apr 8, 2013

Re: Vocabulary

Additionally, bio2rdf.org has identifiers and linked data URIs for most biological entities. Additionally, the URis are easy to predict and generate from existing databases like entrez and uniprot. They either are or are going to use SemanticScience Integrated Ontology (SIO) to represent identifier

RE: Vocabulary

hi amrapali, for human genes, http://www.genenames.org/ cheers, michael Michael Miller Software Engineer Institute for Systems Biology *From:* Bhat, Talapady N. [mailto:talapady.b...@nist.gov] *Sent:* Monday, April 08, 2013 7:26 AM *To:* Amrapali J Zaveri; w3.h...@gmail.com; W3C

RE: Vocabulary

Hi, Have a look at http://xpdb.nist.gov/bioroot/bioroot.pl and type Gene ID. Then you get a list of re-used terms. If you click any of member (shown in blue) of the list, you get another list showing their use. I am not sure whether I have been of much help for you. T N Bhat From: Amrapali J Za

Re: owl:sameAs - Harmful to provenance?

Hi Pat, On 04/04/2013 02:03 AM, Pat Hayes wrote: On Apr 3, 2013, at 9:00 PM, Peter Ansell wrote: On 4 April 2013 11:58, David Booth wrote: On 04/02/2013 05:02 PM, Alan Ruttenberg wrote: On Tuesday, April 2, 2013, David Booth wrote: On 03/27/2013 10:56 PM, Pat Hayes wrote: On Mar 27, 2013, at

[LLD] Today's teleconference at 11AM ET *CANCELLED*

Too many people couldn't make it to the teleconference planned for today to continue discussion about vocabularies for semantic metadata description of datasets. We will have it again next week at the same time: Mon. 11AM ET / 5PM CET (you should have already received an updated calendar event on

Vocabulary

Hi, Please could some one point me to a vocabulary that i could (re-)use to represent Gene ID's, Gene Symbols, Gene Names etc. Thanks. Regards, Amrapali Zaveri http://aksw.org/AmrapaliZaveri

Updated Invitation: Linked Life Data @ Mon 2013-04-15 11:00 - 12:00 (HCLS)

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Canceled Event: Linked Life Data @ Mon 2013-04-08 11:00 - 12:00 (HCLS)

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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