RE: Bio2RDF vs Linked Life Data

Hi,

Thanks, I can do that. I was hoping to also hear about Linked Life Data, so I tried this, more general list.

Bonnie MacKellar
mackellb@stjohns.edu


-----Original Message-----
From: Alexander Garcia Castro [mailto:alexgarciac@gmail.com] 
Sent: Wednesday, June 18, 2014 11:13 AM
To: Bonnie MacKellar
Cc: Muntazir Mehdi; public-lod@w3.org
Subject: Re: Bio2RDF vs Linked Life Data

Bonnie, why dont u address this issue with the bio2rdf mailing list?

On Wed, Jun 18, 2014 at 9:59 AM, Bonnie MacKellar <mackellb@stjohns.edu> wrote:
> Thanks, that is useful! I’ve already taken a look at Bio2RDF Release 
> 3, and it seems promising.
>
>
>
> I think keeping the data up to date is another challenge, at least for 
> some of the datasets. And the problem of broken links – when I first 
> started looking at this, I ran into a LOT of broken links.
>
>
>
> Bonnie MacKellar
>
> mackellb@stjohns.edu
>
>
>
> From: Muntazir Mehdi [mailto:muntazir.75@gmail.com]
> Sent: Wednesday, June 18, 2014 9:18 AM
> To: Bonnie MacKellar
> Cc: Kingsley Idehen; public-lod@w3.org
>
>
> Subject: Re: Bio2RDF vs Linked Life Data
>
>
>
> Hi,
>
>
>
> We at INSIGHT, Ireland are working on discovery of relevant datasets, 
> specifically for Life Sciences use-case. A primary proposed for this 
> purpose is an algorithm used for extraction of keywords (from local 
> datasets), based on which single atomic lookups (no keyword search or 
> any proprietary tool) on LOD datasets can be performed, is already 
> published. Another algorithm, which uses the extracted keywords and 
> queries the LOD datasets, was also accepted recently (not in 
> proceedings yet). In our case, we use datasets listed on Bio2RDF Release2 & 3.
>
> While working on extending the algorithm, i observed that, the data in 
> Bio2RDF has a high overlap (among datasets) and some data is also illegible.
>
> Bonnie, a recent initiative about Bio2RDF Release-3 can be useful for you.
> In my opinion, most of datasets listed there have live sparql 
> endpoints & a clean set of stats are also available. If you are 
> interested in RDF dumps, you can find them there as well.
>
>
>
> Bottom line, IMO, current Life Sciences LOD is clearly not in a very 
> good shape, specially, considering the nature of domain, the 
> reliability factor is very low. However, many fellows are working hard to improve it.
>
>
>
> Cheers,
>
> Mehdi
>
>
>
> On Wednesday, June 18, 2014, Bonnie MacKellar <mackellb@stjohns.edu> wrote:
>
> Hi,
> No I don't know this one.  Is  there any more information?  What is 
> the purpose of this repository? What datasets are cached? I tried 
> clicking on the datasets link in the About tab, but get an error 
> message " Resource /void/Dataset not found.".
>
> So this adds to my confusion. What are the differences between 
> Bio2RDF, Linked Life Data, and OpenLink? Obviously, included datasets, 
> but I have compared Bio2RDF and Linked Life Data on this dimension 
> (and will soon, if I can get a list from OpenLink), but there is a lot 
> of overlap.  Other people must be also facing this choice, no? Are all 
> of these sites stable? Up to date? How well do they work with tools 
> like Silk? What if I eventually want to use a crawler like LSSpider 
> instead of dumps, so that my results stay up to date? I would assume 
> that these are all questions that application developers who want to use Linked Open Data would be asking.
>
> Thanks,
> Bonnie MacKellar
> mackellb@stjohns.edu
>
>
> -----Original Message-----
> From: Kingsley Idehen [mailto:kidehen@openlinksw.com]
> Sent: Wednesday, June 18, 2014 7:52 AM
> To: public-lod@w3.org
> Subject: Re: Bio2RDF vs Linked Life Data
>
> On 6/17/14 5:27 PM, Bonnie MacKellar wrote:
>> Yes, in fact, I have been using a dump from that site for most of my 
>> preliminary work. But there is no working SPARQL endpoint, and there 
>> is often a big gap between dumps. Plus, there are other datasets I 
>> want to use as well.  I am trying to understand the benefits of using 
>> these platforms that bring everything together.
>>
>> Bonnie MacKellar
>> mackellb@stjohns.edu
>
> Have you looked at our live 50 Billion+ triples based LOD Cloud Cache 
> [1] which does include data loaded from these projects, where the data 
> is available as an RDF dump. You can start via a simple keyword search.
>
> Links:
>
> [1] http://lod.openlinksw.com -- LOD Cloud Cache [2] 
> http://lod.openlinksw.com/c/IJ3UOS4 -- Default results page for 
> pattern "Protein"
> [3] http://lod.openlinksw.com/c/GYIJAVW -- Entity Types associated 
> with pattern "Protein"
> [4] http://lod.openlinksw.com/c/GYZPJFS -- Entity Relationship Types
> (Relations) in which an Entity associated with the pattern "Protein"
> plays the role of Subject
> [5] http://lod.openlinksw.com/c/F734UKK -- Entity Relationship Types
> (Relations) in which an Entity associated with the pattern "Protein"
> plays the role of Object.
>
> --
>
> Regards,
>
> Kingsley Idehen
> Founder & CEO
> OpenLink Software
> Company Web: http://www.openlinksw.com Personal Weblog: 
> http://www.openlinksw.com/blog/~kidehen

> Twitter Profile: https://twitter.com/kidehen

> Google+ Profile: https://plus.google.com/+KingsleyIdehen/about

> LinkedIn Profile: http://www.linkedin.com/in/kidehen
>
>
>
>
>
>
> --
>
>
>
> Muntazir Mehdi
>
> Research Intern | Healthcare and Life Sciences Unit
>
> INSIGHT @ NUIG (Formerly DERI), Ireland
>
> Student | Department of Computer Science
>
> Technical University Kaiserslautern, Germany
>
> https://sites.google.com/site/muntazir75/

>
>



--
Alexander Garcia
http://www.alexandergarcia.name/

http://www.usefilm.com/photographer/75943.html

http://www.linkedin.com/in/alexgarciac

Received on Wednesday, 18 June 2014 15:17:51 UTC