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From: BioPortal <ad...@bi...> - 2024-02-17 04:54:45
|
Environment Ontology (ENVO) was processed for use in BioPortal. Here are the results: <br><br> Parsed successfully<br/>Indexed terms for search<br/>Indexed properties for search<br/>Class metrics calculated<br/>Created submission version diff successfully <br><br> Please contact su...@bi... if you have questions. <br><br> The ontology can be <a href="http://bioportal.bioontology.org/ontologies/ENVO">browsed in BioPortal</a>. <br><br> Thank you,<br> The BioPortal Team |
From: John G. <jgr...@st...> - 2020-08-31 23:39:17
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Chris M. <cjm...@lb...> - 2019-06-26 02:24:26
|
GAZ is an open-source gazetteer that is part of the OBO family of resources: http://obofoundry.org/ontology/gaz GAZ has about 600k entries representing different geographic entities, from the Mariannas Trench to Minnesota. Efforts on GAZ have restarted after a period of hiatus. Lynn Schriml has been assigned contact for GAZ. A group of us are attempting to work through various issues on the tracker, including figuring out a better way to manage GAZ in GitHub, linking GAZ to ENVO, and integrating GAZ with Wikidata (and from there, other resources like Geonames). You can follow the tracker here: https://github.com/EnvironmentOntology/gaz/issues Like any OBO ontology, anyone is welcome to post issues or follow the tracker. We also have a mailing list, where amongst other things you will find announcements of regular meetings: https://groups.google.com/forum/#!forum/obo-gazetteer Anyone can sign up, but as with any google group, include a brief message when you sign up, especially if you are using a non-academic email address, so it doesn't look like spam. |
From: Hilmar L. <hl...@ne...> - 2019-01-19 22:26:36
|
( Apologies if you have seen this already. Early registration deadline is only days away. The program includes a session on semantics for biodiversity and environmental sciences: http://us2ts.org/2019/posts/program-session-vi.html <http://us2ts.org/2019/posts/program-session-vi.html> ) =============================================== U.S. Semantic Technologies Symposium Series March 11-13, 2019 Duke University in Durham, NC http://us2ts.org/ <http://us2ts.org/> Early Registration Deadline: January 22, 2019 ================================================ The early registration deadline for the 2nd U.S Semantic Technologies Symposium is coming up on January 22, 2019! Register early to get the best registration rates: http://us2ts.org/2019/posts/registration.html <http://us2ts.org/2019/posts/registration.html> We are also excited to announce two exceptional keynote speakers: Jim Hendler <https://www.linkedin.com/in/jameshendler/> (Rensselaer Polytechnic Institute) and Helena Deus <https://www.linkedin.com/in/helenadeus/> (Elsevier)! The program of the symposium is posted online: http://us2ts.org/2019/posts/program.html <http://us2ts.org/2019/posts/program.html> The detailed program for each session will be published next week. You still have a chance to make a contribution by submitting a lightning talk for one of the two plenary Lightning Talk sessions. The submission for Lightning Talks will be open next week on the US2TS Calls <http://us2ts.org/2019/posts/cfp.html> webpage (http://us2ts.org/2019/posts/cfp.html <http://us2ts.org/2019/posts/cfp.html>). The goal of the U.S. Semantic Technologies Symposium series is to bring together the U.S. Semantic Web community and begin forming such a research network. We achieve this by supporting communication across disciplinary, organizational, and geographical boundaries. The Symposium events provide a forum by which participants can share information and ideas, coordinate ongoing or planned research activities, foster synthesis and new collaborations, develop community standards, and advance their science and education through communication and the sharing of ideas. To this end, the 2019 Symposium will be an informal gathering with plenty of time for discussion and breakout sessions. We encourage anyone with an interest in the Semantic Web, regardless of field, to attend. For all questions please contact the organizers at con...@go... <mailto:con...@go...>. |
From: Lbl <nat...@lb...> - 2018-11-13 20:03:43
|
Excellent. They have great tools. I’m sure as we move forward some of this will become more clear and we can make our gene / disease links public. Nathan > On Nov 13, 2018, at 7:14 PM, Mcgibbney, Lewis J (398M) <Lew...@jp...> wrote: > > Hi Nathan, > Google have been pretty good recently about providing guidance on use of schema.org in pages. Specifically, this time last year they reached out to many data providers across Earth and space sciences e.g. NASA< NOAA, USGS, etc. in a big to have us implement enough schema.org such that they could launch their new dataset search product. To this end they provided guidance as to what they would scrape from a Webpage if it were present. > Their efforts to date can be seen at https://toolbox.google.com/datasetsearch, so across the spectrum a lot of progress has been made. > Google are also a bit better than others in this commercial search space as they at least provide the structured data markup tooling which gives you something to go on. > Lewis > > From: Nathan Dunn <nat...@lb...> > Date: Tuesday, November 13, 2018 at 9:31 AM > To: Ramona Walls <rw...@cy...> > Cc: Chris Mungall <cjm...@lb...>, "obo...@li..." <obo...@li...>, "pie...@aw..." <pie...@aw...>, "mjo...@lb..." <mjo...@lb...>, "Mcgibbney, Lewis J (398M)" <Lew...@jp...> > Subject: Re: DataONE Webinar Series: Schema.org: Improving access to data through a standardized language > > > Just my two cents from being here at bioschema’s and having implemented at the AGR. > > I liked the analogy of it providing data for a “tourist rather than a pilot”. If fields won’t be searched on, in general we are discouraged from showing them, so having a rich and well-defined data model is less important, with the real focus on being SEO and hopefully providing disease associations, which is very different from the way we typically look at data. URLs and ontology terms encouraged, but not required. > > I think the bigger problem is that the target for this is a black-box of search engines that are not necessarily driving the process nor open about what they are doing in the hope that we do the right thing. Would be good if there was an open consumer of this data to help more reliably drive this. > > > Nathan > > > > On Nov 13, 2018, at 3:31 PM, Ramona L. Walls <rw...@cy...> wrote: > > I'm not going to the session, but I heard Adam give a talk on this at ESIP a few months ago. He basically explained how they implemented schema.org. We are already using it at CyVerse, and our pages show up in google data search. I agree, however, that the level of granularity is very low -- simply "subject" keywords. I think it could be combined with bioshema. Not sure if that has taken off. > > We actually have the ability to add ontology terms as metadata, but - beyond a very specific use case - haven't figured out a good way to get people to add it yet. > > Ramona > ------------------------------------------------------ > Ramona L. Walls, Ph.D. > Senior Scientific Analyst > CyVerse > rw...@cy... > www.cyverse.org > Biosciences Research Laboratory > > 1601 East Helen St > Tucson, AZ 85721 > tel: 520-626-1489 > fax: 520-626-4824 > > > On Mon, Nov 12, 2018 at 11:24 AM Chris Mungall <cjm...@lb...> wrote: > I notice there is a DataONE webinar tomorrow on schema.org > > https://dataone.zoom.us/webinar/register/WN_glwB-swkQxmLY3ZbfJ8YIg?utm_source=newsletter&utm_medium=email&utm_campaign=dataone_webinar_series_schemaorg_improving_access_to_data_through_a_standardized_language&utm_term=2018-11-11 > > I won't make it but curious if any ENVOers plan on attending. > > I am skeptical as to whether schema.org will suffice as a standardized > language for the life sciences or environmental sciences. It's > granularity is poor and it's not very science-focused. The bioschemas > people have been trying to enhance it with more biology, but my > understanding is that the sum of current efforts is managing to get a > small handful of additional classes in, which does not suffice. > > Ontologies such as ENVO and SWEET should form the standardized language. > Of course, for SEO purposes people will want to index as much as > possible with schema.org but we need a strategy for more granular data. > > |
From: Mcgibbney, L. J (398M) <Lew...@jp...> - 2018-11-13 18:14:25
|
Hi Nathan, Google have been pretty good recently about providing guidance on use of schema.org in pages. Specifically, this time last year they reached out to many data providers across Earth and space sciences e.g. NASA< NOAA, USGS, etc. in a big to have us implement enough schema.org such that they could launch their new dataset search product. To this end they provided guidance as to what they would scrape from a Webpage if it were present. Their efforts to date can be seen at https://toolbox.google.com/datasetsearch, so across the spectrum a lot of progress has been made. Google are also a bit better than others in this commercial search space as they at least provide the structured data markup tooling which gives you something to go on. Lewis From: Nathan Dunn <nat...@lb...> Date: Tuesday, November 13, 2018 at 9:31 AM To: Ramona Walls <rw...@cy...> Cc: Chris Mungall <cjm...@lb...>, "obo...@li..." <obo...@li...>, "pie...@aw..." <pie...@aw...>, "mjo...@lb..." <mjo...@lb...>, "Mcgibbney, Lewis J (398M)" <Lew...@jp...> Subject: Re: DataONE Webinar Series: Schema.org: Improving access to data through a standardized language Just my two cents from being here at bioschema’s and having implemented at the AGR. I liked the analogy of it providing data for a “tourist rather than a pilot”. If fields won’t be searched on, in general we are discouraged from showing them, so having a rich and well-defined data model is less important, with the real focus on being SEO and hopefully providing disease associations, which is very different from the way we typically look at data. URLs and ontology terms encouraged, but not required. I think the bigger problem is that the target for this is a black-box of search engines that are not necessarily driving the process nor open about what they are doing in the hope that we do the right thing. Would be good if there was an open consumer of this data to help more reliably drive this. Nathan On Nov 13, 2018, at 3:31 PM, Ramona L. Walls <rw...@cy...<mailto:rw...@cy...>> wrote: I'm not going to the session, but I heard Adam give a talk on this at ESIP a few months ago. He basically explained how they implemented schema.org<http://schema.org/>. We are already using it at CyVerse, and our pages show up in google data search. I agree, however, that the level of granularity is very low -- simply "subject" keywords. I think it could be combined with bioshema. Not sure if that has taken off. We actually have the ability to add ontology terms as metadata, but - beyond a very specific use case - haven't figured out a good way to get people to add it yet. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Senior Scientific Analyst CyVerse rw...@cy...<mailto:rw...@cy...> www.cyverse.org<http://www.cyverse.org/> Biosciences Research Laboratory 1601 East Helen St Tucson, AZ 85721 tel: 520-626-1489 fax: 520-626-4824 On Mon, Nov 12, 2018 at 11:24 AM Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> wrote: I notice there is a DataONE webinar tomorrow on schema.org<http://schema.org/> https://dataone.zoom.us/webinar/register/WN_glwB-swkQxmLY3ZbfJ8YIg?utm_source=newsletter&utm_medium=email&utm_campaign=dataone_webinar_series_schemaorg_improving_access_to_data_through_a_standardized_language&utm_term=2018-11-11 I won't make it but curious if any ENVOers plan on attending. I am skeptical as to whether schema.org<http://schema.org/> will suffice as a standardized language for the life sciences or environmental sciences. It's granularity is poor and it's not very science-focused. The bioschemas people have been trying to enhance it with more biology, but my understanding is that the sum of current efforts is managing to get a small handful of additional classes in, which does not suffice. Ontologies such as ENVO and SWEET should form the standardized language. Of course, for SEO purposes people will want to index as much as possible with schema.org<http://schema.org/> but we need a strategy for more granular data. |
From: Mcgibbney, L. J (398M) <Lew...@jp...> - 2018-11-13 18:11:15
|
Hi Chris, This topic is ripe for us really making further progress at this Winter's ESIP Meeting https://www.esipfed.org/meetings/upcoming-meetings/wm19 We will be hosting a GeoSemantics Symposium the day before ESIP starts and this topic will be the primary focus. A lot of progress has been made in this space to bring it back to a stage where people are yet again interested in the topic however as you mention, the domain specific extensions are where the real value will be gained. The schema.org documentation on the extension of the core vocabulary can be found at https://schema.org/docs/extension.html I suspect that most of the extensions we end up developing will ultimately be external extensions. However examples of reviewed hosted extensions can be found at https://schema.org/docs/schemas.html I would be very happy to take this conversation to the esip-semtech mailing list as it is highly relevant for our roadmap. Thanks for including me in this thread. Lewis Dr. Lewis John McGibbney Ph.D., B.Sc. Data Scientist II Computer Science for Data Intensive Applications Group (398M) Instrument Software and Science Data Systems Section (398) Jet Propulsion Laboratory California Institute of Technology 4800 Oak Grove Drive Pasadena, California 91109-8099 Mail Stop : 158-256C Tel: (+1) (818)-393-7402 Cell: (+1) (626)-487-3476 Fax: (+1) (818)-393-1190 Email: lew...@jp... ORCID: orcid.org/0000-0003-2185-928X Dare Mighty Things On 11/12/18, 10:24 AM, "Chris Mungall" <cjm...@lb...> wrote: I notice there is a DataONE webinar tomorrow on schema.org https://dataone.zoom.us/webinar/register/WN_glwB-swkQxmLY3ZbfJ8YIg?utm_source=newsletter&utm_medium=email&utm_campaign=dataone_webinar_series_schemaorg_improving_access_to_data_through_a_standardized_language&utm_term=2018-11-11 I won't make it but curious if any ENVOers plan on attending. I am skeptical as to whether schema.org will suffice as a standardized language for the life sciences or environmental sciences. It's granularity is poor and it's not very science-focused. The bioschemas people have been trying to enhance it with more biology, but my understanding is that the sum of current efforts is managing to get a small handful of additional classes in, which does not suffice. Ontologies such as ENVO and SWEET should form the standardized language. Of course, for SEO purposes people will want to index as much as possible with schema.org but we need a strategy for more granular data. |
From: Nathan D. <nat...@lb...> - 2018-11-13 17:31:23
|
Just my two cents from being here at bioschema’s and having implemented at the AGR. I liked the analogy of it providing data for a “tourist rather than a pilot”. If fields won’t be searched on, in general we are discouraged from showing them, so having a rich and well-defined data model is less important, with the real focus on being SEO and hopefully providing disease associations, which is very different from the way we typically look at data. URLs and ontology terms encouraged, but not required. I think the bigger problem is that the target for this is a black-box of search engines that are not necessarily driving the process nor open about what they are doing in the hope that we do the right thing. Would be good if there was an open consumer of this data to help more reliably drive this. Nathan > On Nov 13, 2018, at 3:31 PM, Ramona L. Walls <rw...@cy...> wrote: > > I'm not going to the session, but I heard Adam give a talk on this at ESIP a few months ago. He basically explained how they implemented schema.org <http://schema.org/>. We are already using it at CyVerse, and our pages show up in google data search. I agree, however, that the level of granularity is very low -- simply "subject" keywords. I think it could be combined with bioshema. Not sure if that has taken off. > > We actually have the ability to add ontology terms as metadata, but - beyond a very specific use case - haven't figured out a good way to get people to add it yet. > > Ramona > ------------------------------------------------------ > Ramona L. Walls, Ph.D. > Senior Scientific Analyst > CyVerse > rw...@cy... <mailto:rw...@cy...> > <>www.cyverse.org <http://www.cyverse.org/> > Biosciences Research Laboratory > 1601 East Helen St > Tucson, AZ 85721 > tel: 520-626-1489 <> > fax: 520-626-4824 <> > > On Mon, Nov 12, 2018 at 11:24 AM Chris Mungall <cjm...@lb... <mailto:cjm...@lb...>> wrote: > I notice there is a DataONE webinar tomorrow on schema.org <http://schema.org/> > > https://dataone.zoom.us/webinar/register/WN_glwB-swkQxmLY3ZbfJ8YIg?utm_source=newsletter&utm_medium=email&utm_campaign=dataone_webinar_series_schemaorg_improving_access_to_data_through_a_standardized_language&utm_term=2018-11-11 <https://dataone.zoom.us/webinar/register/WN_glwB-swkQxmLY3ZbfJ8YIg?utm_source=newsletter&utm_medium=email&utm_campaign=dataone_webinar_series_schemaorg_improving_access_to_data_through_a_standardized_language&utm_term=2018-11-11> > > I won't make it but curious if any ENVOers plan on attending. > > I am skeptical as to whether schema.org <http://schema.org/> will suffice as a standardized > language for the life sciences or environmental sciences. It's > granularity is poor and it's not very science-focused. The bioschemas > people have been trying to enhance it with more biology, but my > understanding is that the sum of current efforts is managing to get a > small handful of additional classes in, which does not suffice. > > Ontologies such as ENVO and SWEET should form the standardized language. > Of course, for SEO purposes people will want to index as much as > possible with schema.org <http://schema.org/> but we need a strategy for more granular data. |
From: Ramona L. W. <rw...@cy...> - 2018-11-13 14:51:53
|
I'm not going to the session, but I heard Adam give a talk on this at ESIP a few months ago. He basically explained how they implemented schema.org. We are already using it at CyVerse, and our pages show up in google data search. I agree, however, that the level of granularity is very low -- simply "subject" keywords. I think it could be combined with bioshema. Not sure if that has taken off. We actually have the ability to add ontology terms as metadata, but - beyond a very specific use case - haven't figured out a good way to get people to add it yet. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Senior Scientific Analyst *CyVerse* rw...@cy... www.cyverse.org Biosciences Research Laboratory 1601 East Helen St Tucson, AZ 85721 tel: 520-626-1489 fax: 520-626-4824 On Mon, Nov 12, 2018 at 11:24 AM Chris Mungall <cjm...@lb...> wrote: > I notice there is a DataONE webinar tomorrow on schema.org > > > https://dataone.zoom.us/webinar/register/WN_glwB-swkQxmLY3ZbfJ8YIg?utm_source=newsletter&utm_medium=email&utm_campaign=dataone_webinar_series_schemaorg_improving_access_to_data_through_a_standardized_language&utm_term=2018-11-11 > > I won't make it but curious if any ENVOers plan on attending. > > I am skeptical as to whether schema.org will suffice as a standardized > language for the life sciences or environmental sciences. It's > granularity is poor and it's not very science-focused. The bioschemas > people have been trying to enhance it with more biology, but my > understanding is that the sum of current efforts is managing to get a > small handful of additional classes in, which does not suffice. > > Ontologies such as ENVO and SWEET should form the standardized language. > Of course, for SEO purposes people will want to index as much as > possible with schema.org but we need a strategy for more granular data. > |
From: Chris M. <cjm...@lb...> - 2018-11-12 18:24:24
|
I notice there is a DataONE webinar tomorrow on schema.org https://dataone.zoom.us/webinar/register/WN_glwB-swkQxmLY3ZbfJ8YIg?utm_source=newsletter&utm_medium=email&utm_campaign=dataone_webinar_series_schemaorg_improving_access_to_data_through_a_standardized_language&utm_term=2018-11-11 I won't make it but curious if any ENVOers plan on attending. I am skeptical as to whether schema.org will suffice as a standardized language for the life sciences or environmental sciences. It's granularity is poor and it's not very science-focused. The bioschemas people have been trying to enhance it with more biology, but my understanding is that the sum of current efforts is managing to get a small handful of additional classes in, which does not suffice. Ontologies such as ENVO and SWEET should form the standardized language. Of course, for SEO purposes people will want to index as much as possible with schema.org but we need a strategy for more granular data. |
From: John G. <jgr...@st...> - 2018-03-22 09:03:37
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Chris M. <cjm...@lb...> - 2016-12-22 16:27:27
|
Hi all, This list has been in existence since the inception of EnvO, it doesn't see much traffic these days. I know many of you subscribe to the github repo here: https://github.com/EnvironmentOntology/envo/ (if you want to, click where it says "Watch". You will need a github account) This is a great way of hearing about new term requests or for joining discussions about modeling. Many of you also subscribe to the EnvO twitter feed http://twitter.com/envoTweets This is a great way to hear EnvO-related news. For example, this paper in PeerJ by Evangelos Pafilis and colleagues on using EnvO for exploration of microbial community sequence data https://peerj.com/articles/2690/ Would people still be interested in hearing updates and having discussions on this list? If so, we can occasionally repost things of particular interest from either the twitter feed or github here. New releases? Should we do more to promote the list to encourage a community? Should we have more GSC people on here? Either way I encourage anyone and everyone to post their EnvO-related questions, thoughts, concerns on one of these media! For now I am changing the settings of this list so that postings from unsubscribed people are immediately rejected. Currently they are held in a moderator queue which I comb through at increasingly longer durations. Let me know if there is interest in keeping the list more open and we can see about having a volunteer rota (it only takes a few seconds to do the moderation, but this adds up for multiple mail lists). Happy holidays! |
From: Chris M. <cjm...@lb...> - 2016-04-18 21:37:28
|
The theme of this year's ICBO is "Food, Nutrition, Health and Environment for the 9 billion", so it should of interest to everyone on this list. http://icbo.cgrb.oregonstate.edu/ We are currently soliciting submissions of novel (not previously published nor concurrently submitted) research papers that describe major advances in the field of biological and biomedical ontologies, report and/or discuss a new ontology, a major revision or extension to an existing ontology, new applications of an existing ontology or a potentially new ontology, a substantial critique of an existing ontology with a proposed alternative approach, the result of applying an ontology - for example, data interoperability, data sharing, BIG-data analysis, high-throughput methods, novel analytical reasoners, annotated resources, etc. Submission Process There are separate guidelines and submission portals for ICBO and BioCreative. Therefore, please follow the instructions carefully on the conference website: http://icbo.cgrb.oregonstate.edu/submission How to select between ICBO and BioCreative submission? If you are submitting the papers and abstracts on ontologies and related applications, ICBO is your choice. For machine learning and text mining of biological data, your choice is BioCreative. If the work includes both (machine learning, text mining, and ontologies), please select the ICBO for paper/poster submission Key Dates 4/25/2016 Scientific Paper submission deadline (ICBO only) 4/25/2016 Extended Scientific Abstract submission deadline (BioCreative only) 5/15/2016 Extended Scientific Poster Abstract submission deadline (ICBO only) |
From: Jaiswal, P. - O. <jai...@sc...> - 2016-02-22 22:51:49
|
_______________________________________________ go-ontology mailing list go-...@li... https://mailman.stanford.edu/mailman/listinfo/go-ontology |
From: Pier L. B. <pbu...@mp...> - 2015-09-09 08:57:18
|
Hello Ben, Following up on Chris' response, I've created an issue on our GitHub tracker for you to add any more classes you'd like in ENVO: https://github.com/EnvironmentOntology/envo/issues/249 We've recently released our environmental process branch (which is nascent, and subject to rapid change) where many of the requested classes will be placed. Some of your requests have already been added and are ready for feedback/revision. Best, Pier On Mon, 10 Aug 2015 06:55:53 -1000, Ben Livneh <ben...@co...> wrote: > Hello, > > My name is Ben Livneh and recently I've had a paper accepted to Nature > Scientific Data, where the copy editor had a hard time finding the > appropriate terms to describe my data set for near-surface temperature, > precipitation, and other derived entities, like streamflow, > evapotranspiration, etc. using your data base. > I'd like to offer my assistance to help you update the data base of > official terms. If you can help my navigate to the correct spot that would > be appreciated. I'm happy to discuss further. > Best, > Ben -- Dr. Pier Luigi Buttigieg HGF-MPG Group for Deep Sea Ecology and Technology Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung c/o Max Planck Institute for Marine Microbiology Celsiusstrasse 1, 28359 Bremen, Germany Tel: +49 421 2028 984 Email: pbu...@mp... |
From: Chris M. <cjm...@lb...> - 2015-08-25 19:51:26
|
Forwarded message: > From: Robert Hoehndorf <rob...@ka...> > To: obo...@li... > Subject: [Obo-discuss] Postdoc position: Semantic integration in > marine biodiversity > Date: Tue, 25 Aug 2015 16:21:17 +0300 > > > An opening for a post-doctoral researcher is available in the group of > Robert Hoehndorf at the Computational Bioscience Research Center, King > Abdullah University of Science and Technology, Thuwal, Saudi Arabia. > > Start date: Earliest possible > Location: Thuwal, Saudi Arabia > Employment: Full-time > Duration: initial contract 1 year (renewable up to 3 years) > > Applications are accepted until the position is filled. > > Job description: > > We are seeking to fill a position for a postdoctoral researcher > working on data integration for marine microorganisms. > > The postdoctoral researcher will join a large collaborative project in > synthetic biology aimed at rational design of microbial cell > factories. The postdoctoral researcher will be responsible for > integrating information about marine microorganisms, spanning > molecular information, phenotype, geolocation and environment. > > The ideal candidate will either have a background in biological > ontologies and data integration using Semantic Web technologies, or a > background in marine microbiology with a strong interest in developing > ontologies and integrated resources for microorganisms. > > The postdoctoral researcher will be responsible for carrying out > research independently and collaboratively with other members of the > research group, and present research results at conferences and in > scientific journals. > > The researcher will work in the group of Prof Robert Hoehndorf > (http://www.kaust.edu.sa/faculty/hoehndorf.html), a research group > which is recognized for its work on biomedical ontologies, and which > has strong collaborations with leading international research > institutes. > > Expertise required: > - PhD in computer science, biology, bioinformatics, or a related field > (obtained in the last 5 years) > - Programming skills (preferably Java or C/C++, or a scripting > language (Python, Perl, Groovy, etc.)) > > Desirable: > - Experience in marine biodiversity and microbiology > - Experience with ontologies in biology or biomedicine > - Experience with Semantic Web technologies (RDF, OWL, SPARQL) > > > Postdoctoral researchers are entitled to a competitive salary > (commensurate with the applicant's qualifications), free, > fully-furnished housing on the KAUST campus, free medical and life > insurance, free education at KAUST schools for the postdoctoral > researchers' children, and relocation allowance. > > > KAUST will be responsible for the actual recruiting decision, > appointment offers and employment benefits. > > > How to apply: > > To apply, please send your CV, a list of publications, the names and > contact details of two referees, and a brief letter of motivation by > email to: rob...@ka... > > Contact: > > For any questions related to the position, please contact Robert > Hoehndorf (rob...@ka...). > > > About KAUST: > > King Abdullah University of Science and Technology (KAUST) is an > international, graduate-level research university dedicated to > inspiring a new age of scientific achievement in the Kingdom of Saudi > Arabia, in the region, and around the globe. As an independent, > merit-based institution, KAUST's pioneering matrix structure of > academic divisions and interdisciplinary research centers enables top > researchers from around the globe and across all cultures to work > together to solve challenging scientific and technological issues. > > The KAUST global research and education networks support diverse > talents, both on its campus and at other premier universities and > research institutions, through collaborative research agreements, > grants, and student scholarship programs. KAUST, open to both men and > women from all around the world, is governed by an independent, > self-perpetuating Board of Trustees. The core campus, located on more > than 36 million square meters on the Red Sea at Thuwal, Saudi Arabia, > was inaugurated on the 23rd of September 2009. > > ------------------------------------------------------------------------------ > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss |
From: Chris M. <cjm...@lb...> - 2015-08-23 19:43:31
|
Hi Ben, Apologies your email was stuck in the moderation queue for two weeks (this can happen if you email using a different account than the one you subscribed with). We definitely welcome any and all assistance. This can be in any way you please You can file individual tickets using our issue tracker (you will need a github account) https://github.com/EnvironmentOntology/envo/issues/ If you have a large set of terms already then spreadsheets or any other kind of document works well too. We can also set up a call to discuss this if you like. This is quite timely. Previously we have focused on physical entities and material, e.g. soil, but for a number of reasons we are expanding in to processes and conditions; you probably won't find many terms like precipitation in the current release of ENVO, but some will be in the next release. On 10 Aug 2015, at 9:55, Ben Livneh wrote: > Hello, > > My name is Ben Livneh and recently I've had a paper accepted to Nature > Scientific Data, where the copy editor had a hard time finding the > appropriate terms to describe my data set for near-surface > temperature, > precipitation, and other derived entities, like streamflow, > evapotranspiration, etc. using your data base. > I'd like to offer my assistance to help you update the data base of > official terms. If you can help my navigate to the correct spot that > would > be appreciated. I'm happy to discuss further. > Best, > Ben > > > -- > Ben Livneh, Ph.D > Assistant Professor, Department of Civil, Environmental, and > Architectural > Engineering > & > Fellow, Cooperative Institute for Research in Environmental Sciences > (CIRES) > Campus Box 216 UCB, Ekely S250C, University of Colorado, Boulder > 80309, USA > Phone: 303-735-0288 | http://www.colorado.edu/ceae/ben-livneh > ------------------------------------------------------------------------------ > _______________________________________________ > Obo-envo mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-envo |
From: Ben L. <ben...@co...> - 2015-08-10 16:56:21
|
Hello, My name is Ben Livneh and recently I've had a paper accepted to Nature Scientific Data, where the copy editor had a hard time finding the appropriate terms to describe my data set for near-surface temperature, precipitation, and other derived entities, like streamflow, evapotranspiration, etc. using your data base. I'd like to offer my assistance to help you update the data base of official terms. If you can help my navigate to the correct spot that would be appreciated. I'm happy to discuss further. Best, Ben -- Ben Livneh, Ph.D Assistant Professor, Department of Civil, Environmental, and Architectural Engineering & Fellow, Cooperative Institute for Research in Environmental Sciences (CIRES) Campus Box 216 UCB, Ekely S250C, University of Colorado, Boulder 80309, USA Phone: 303-735-0288 | http://www.colorado.edu/ceae/ben-livneh |
From: Chris M. <cjm...@lb...> - 2015-03-19 22:52:31
|
On 18 Mar 2015, at 4:39, Pier Luigi Buttigieg wrote: > Hi Chris, > > On Tue, 17 Mar 2015 10:17:12 -0700, "Chris Mungall" <cjm...@lb...> > wrote: >> I'm not involved in publicising this but thought it might be of interest >> to some people here. Do we have any requirements useful to feed in? Or >> are basic qualititive mereological primitives such as part_of and >> overlaps sufficient for reasoning using ENVO? > > I think it would be a good idea to explore a more developed approach, to > capture instance-level scenarios such as some entity influencing an > environment at a distance through, e.g., pollutants running downstream. > This would be a good place to voice such ideas. > > Bringing GAZ into this discussion would, of course, be very relevant. > Additionally, through this point... > >>> * seeking insight on what needs to complement location to meet >>> e-science needs (time?, feature?, event?, process? granularity?). > > ... ENVO can be linked quite nicely. Especially with regards to the feature > and process (which both could be associated with some granularity). > It would also be interesting to hear what needs and targets the geospatial > community have and how ENVO can/should develop to meet them. > > [...] |
From: Pier L. B. <pbu...@mp...> - 2015-03-18 12:06:32
|
Hi Chris, On Tue, 17 Mar 2015 10:17:12 -0700, "Chris Mungall" <cjm...@lb...> wrote: > I'm not involved in publicising this but thought it might be of interest > to some people here. Do we have any requirements useful to feed in? Or > are basic qualititive mereological primitives such as part_of and > overlaps sufficient for reasoning using ENVO? I think it would be a good idea to explore a more developed approach, to capture instance-level scenarios such as some entity influencing an environment at a distance through, e.g., pollutants running downstream. This would be a good place to voice such ideas. Bringing GAZ into this discussion would, of course, be very relevant. Additionally, through this point... >> * seeking insight on what needs to complement location to meet >> e-science needs (time?, feature?, event?, process? granularity?). ... ENVO can be linked quite nicely. Especially with regards to the feature and process (which both could be associated with some granularity). It would also be interesting to hear what needs and targets the geospatial community have and how ENVO can/should develop to meet them. [...] |
From: Chris M. <cjm...@lb...> - 2015-03-17 17:43:15
|
I'm not involved in publicising this but thought it might be of interest to some people here. Do we have any requirements useful to feed in? Or are basic qualititive mereological primitives such as part_of and overlaps sufficient for reasoning using ENVO? Forwarded message: > From: Janna Hastings <has...@eb...> > To: bfo...@go... > Subject: [bfo-discuss] Summer Institute 2015 Call for Participation: > Spatial Ontologies for e-Science > Date: Tue, 17 Mar 2015 15:56:17 -0000 > > Call for Participation > > The Vespucci Initiative for the Advancement of Geographic Information > Science and IAOA is announcing the > 2015 Summer Institute: > > Spatial Ontologies for e-Science > June 21-27, 2015 > Bar Harbor, Maine, USA > > Programme: > Location often acts as an integrator in science, bringing together > perspectives across multiple disciplines and scales. For example, > health scientists increasingly focus on where patients spend their > time, pulling a large variety of environmental and social data into > their analyses. With big data and e-science, this trend has > accelerated and gets increasingly supported through knowledge > infrastructures and associated ontologies. Yet, it is often unclear > how knowledge about location and other spatial properties should best > be captured, and there is only a very limited choice of spatial > ontologies. This Vespucci Institute will ask why this is so and why > there seems to have been so little progress over the past decade. It > will push the frontiers on spatial ontologies for e-science by > > * identifying the gaps between the spatial ontologies that the > e-science community needs and what is currently available from the > ontology community; > * addressing key gaps through hands-on ontology design on site; > * discussing the impact of Linked Open Data on e-science and the > role > of space in this context; > * collecting criteria and techniques for evaluating spatial > ontologies in e-science; > * broadening the discussion of ontology quality and ontology > applications; > * learning to separate approaches that work from those that do not; > * reviewing the work of relevant standards organizations like W3C > and > OGC; > * seeking insight on what needs to complement location to meet > e-science needs (time?, feature?, event?, process? granularity?). > > Facilitators > Peter Fox (Rensselaer Polytechnic Institute) Michael Gruninger > (University of Toronto) Werner Kuhn (University of California, Santa > Barbara) > > > Participants from all sectors of e-science, ontology engineering, and > geospatial as well as other spatial sciences are invited to interact > from > June 22 to 26, 2015, in beautiful Bar Harbor, Maine. As always, the > Vespucci > Institute will challenge the state of the art through lively > discussions and > hands-on problem solving rather than lengthy presentations. > > > Travel and attendance grants are available Deadline for applications: > 15 > April 2015 More information, programme and registration on > http://www.vespucci.org > > > -- > You received this message because you are subscribed to the Google > Groups "BFO Discuss" group. > To unsubscribe from this group and stop receiving emails from it, send > an email to bfo...@go.... > To post to this group, send email to bfo...@go.... > Visit this group at http://groups.google.com/group/bfo-discuss. > For more options, visit https://groups.google.com/d/optout. |
From: Erick A. <eri...@gm...> - 2015-01-29 14:33:38
|
*** Apologies for cross-posting *** Dear colleagues, friends, We have three open positions (located in Ghent, Belgium): 1. CLS BioInformatics Researcher <https://mybayerjob.bayerbbs.com/sap/bc/erecruiting/posting_apply?param=cG9zdF9pbnN0X2d1aWQ9MDA1MDU2ODkwMEI0MUVFNEE5REIzNzgxOUMwRDAzMjgmY2FuZF90eXBlPQ%3d%3d&sap-client=005&sap-language=EN> (2 year contract) 2. CLS Phenotyping Researcher <https://mybayerjob.bayerbbs.com/sap/bc/erecruiting/posting_apply?param=cG9zdF9pbnN0X2d1aWQ9MDA1MDU2ODkwMEI0MUVFNEE5REFGMjVGRkFBMzgxODMmY2FuZF90eXBlPQ%3d%3d&sap-client=005&sap-language=EN> (2 year contract) 3. Computational scientist <https://mybayerjob.bayerbbs.com/sap/bc/erecruiting/posting_apply?param=cG9zdF9pbnN0X2d1aWQ9MDA1MDU2ODkwMEI0MUVENEE5REE2Mzg4NEU2M0RERDYmY2FuZF90eXBlPQ%3d%3d&sap-client=005&sap-language=EN> (permanent contract) If you need more informartion, please contact me (eri...@ba...). Best regards, Erick Antezana |
From: Chris M. <cjm...@lb...> - 2014-12-20 00:10:43
|
ENVO TermGenie is now available * Templated requests: http://envo.termgenie.org/ * Freeform requests: http://envo.termgenie.org/TermGenieFreeForm.html For a description of TermGenie, please see: * http://www.jbiomedsem.com/content/5/1/48/ Currently the only templated requests available are for environmental systems, but others can be added on request. If you have an interest in contributing to ENVO and would like access, then sign up for a persona account (you don't need to do this if you use another termgenie, such as the cell ontology or biological attribute one) and then contact Pier and myself. |
From: Ben A. <b....@au...> - 2014-01-31 03:32:59
|
Semantics for Biodiversity -- call for papers February 28, 2014 - Paper submission deadline (updated) The study of biodiversity examines the richness and variety of life on Earth across multiple organizational and spatial scales, ranging from genomic to organismal through populations and ecosystems; and from local to global scales. Presently, biodiversity observational data are collected by scientists around the world using a diverse set of methods and stored in a variety of formats. Because the problems that biodiversity scientists are investigating are time-critical, societally-relevant, and often global in scale, there is a pressing need to enable scientists to better share, discover, and synthesize biodiversity data from multiple sources. Modern semantic technologies provide a promising way to accomplish this, by capturing rich representations of biodiversity data in ways that afford maximum interoperability and detailed description for re-use. The goal of this special issue is to bring together a collection of papers on biodiversity semantics - to present current state-of-the-art semantic efforts in representing biodiversity data, to spur advances in semantic technologies for biodiversity research, and to help define a common strategy for advancing semantic approaches for describing biodiversity, including considerations about the broader ecological and environmental contexts that inform biodiversity investigations. Semantic approaches for describing biodiversity data are currently being explored on several fronts. The international-scope Biodiversity Information Standards (TDWG) group has developed metadata standards such as Darwin Core (specimen data), ABCD (biological collections), the Taxonomic Concept Schema (names and concepts), and the proposed Audubon Core (biodiversity multimedia). Darwin Core is very broadly accepted as a transfer schema for sharing biodiversity data, and is the standard adopted by GBIF, the Global Biodiversity Information Facility - that currently aggregates over 400 million biodiversity records from collections around the world. However, all current TDWG standards are lacking in semantic expressivity and compatibility with reasoning requirements for effective knowledge representation and reasoning (KRR), and tend to focus on observations of specimens without descriptions of their environmental context. In parallel, the Earth and environmental science community, through emerging efforts like NSF's EarthCube, will be developing semantic models for describing environmental systems and processes. The genomics community also has a growing interest in linking biodiversity information to genetic samples. For example, metagenomics research often involves collection of aggregate samples of biodiversity, such as an amount of soil or ocean water, where genetic sequencing then provides a characterization of the variety of microbial and other life forms that are in the sample. Under the banner term of phenotype ontologies, research communities focusing on model organisms and (increasingly) broader taxonomic groups have assembled structured vocabularies for anatomical features that permit reasoning and integration with genomics and evolutionary analyses. Clarifying the semantics of biodiversity will provide an essential linchpin among investigations that enable us to understand how environmental factors, both biotic and abiotic, influence phenotype, community composition, and species' ranges and viability, as well as provide insights into the evolutionary relationships among Earth's life forms. This special issue calls for original papers describing the latest developments, trends, and solutions for biodiversity semantics and its applications. The topics of interests include, but are not limited to: * Formal models of biodiversity - specimens, occurrences, samples, etc. * Taxonomic and nomenclatural semantics, classification representation and provenance * Field observation and measurement semantics * Semantic approaches for enhancing discovery of biodiversity data * Interoperability of biodiversity with Earth and environmental science data * Linking taxonomic with trait and genomic data * Semantic representations of phylogenetic data * Semantic descriptions of biodiversity models and semantic approaches to support model-data confrontation * Integration of species, ecosystems, and genetic level data * Semantics of populations, communities, and ecosystem services * Data integration for critical zone studies * Geospatial semantics for biodiversity - locations, ranges, co-occurrences, etc. * Software for semantic annotation of biodiversity data * Bottom-up biodiversity ontology development * Ontology design patterns and methods for ontology evolution for biodiversity * Linked Open Data (LOD) for biodiversity * Representing provenance of biodiversity data * Limitations of, alternatives to, and extensions to Semantic Web languages and methodologies to serve biodiversity research needs Submissions February 28, 2014 - Paper submission deadline (updated) Submissions shall be made through the Semantic Web journal website at http://www.semantic-web-journal.net<http://www.semantic-web-journal.net/>. Note that you need to request an account on the website for submitting a paper. Please indicate in the cover letter that it is for the Semantics for Biodiversity special issue. Submissions are possible in all standing paper type of the journal, see http://www.semantic-web-journal.net/authors for descriptions: full research papers, surveys, linked dataset descriptions, ontology descriptions, application reports, tool/systems reports. Guest editors Benjamin Adams (The University of Auckland, New Zealand) Nico Franz (Arizona State University) Birgitta König-Ries (Friedrich Schiller University Jena) Deborah McGuinness (Rensselaer Polytechnic Institute) Mark Schildhauer (NCEAS, University of California, Santa Barbara) |
From: Chris M. <cjm...@lb...> - 2013-12-21 19:55:03
|
http://www.jbiomedsem.com/content/4/1/43/abstract |