[esip-semantictech] Ecology ontologies

Sat Jul 14 07:46:34 EDT 2018

Hi all,

Picking up on Mark's response:

ENVO, PCO (still online, now on GitHub [1]), and other 
environmental/ecology themed ontologies had requests in this direction, 
so we put together ECOCORE at a Hackathon lead by Anne Thessen (in CC).

https://github.com/EcologicalSemantics/ecocore

@Justin: you're getting a 404 on the PURL because we haven't made the 
first official release yet. We can accelerate this if there's a use case 
on a timeline and also welcome co-editors and contributors.

ECOCORE reuses many others for compatibility and is developed along OBO 
best practices. It will pull in the scattered eco-themed terms in the 
OBO world (e.g. behaviours, ecosystem types, assemblages) and extend it 
to cover more core ecological entities (trophic types, ecosystem roles, 
etc).

We'll be working with the developers of the Essential Biodiversity 
Variables (EBVs) and similar frameworks to help prioritise content 
creation. If you have a set of terms that are needed, please let us 
know. Posting issues on the tracker is probably the best way to 
communicate here.

Best,
Pier

[2] https://github.com/PopulationAndCommunityOntology/pco

On 13/07/2018 23:57, Mark Schildhauer via esip-semanticweb wrote:
> Hi folks,
> Just wanted to chip-in that the US NSF-sponsored "Arctic Data Center" 
> repository (http://arcticdata.io) as well as DataONE 
> (http://dataone.org) are also developing ecological ontologies 
> (RDF/OWL), building from the framework provided by ENVO, that is 
> currently being aligned with SWEET.
> 
> Our specific initial focus is on ecosystems carbon-cycling phenomena, 
> and we are close to unveiling our work. It heavily imports terms from 
> ENVO, that in turn is OBO Foundry-compliant so is importing terms 
> (Classes, Object Properties) etc from PATO, RO, UO, IAO, BFO, etc.  In 
> addition we are playing close attention to assure compatibility with 
> schema.org <http://schema.org> terms, and incorporating 
> Observations&Measurements models (e.g. O&M and OBOÉ) to facilitate using 
> our ontology to semantically annotate ecological data.
> 
> Matt Jones and I will be at the upcoming ESIP meeting in Tucson next 
> week if anyone walks to learn about our progress, or finds ways to 
> synergize/collaborate!
> 
> thanks.
> 
> cheers,
> Mark
> -----
> Mark Schildhauer, PhD
> Director of Computing (ret.)
> Co-PI, Arctic Data Center
> Co-PI, LTER Network Communications Office
> National Center for Ecological Analysis and Synthesis, NCEAS, UCSB
> 735 State St., Suite 300
> Santa Barbara CA 93101
> Email: schild at nceas dot ucsb dot edu
> Web: http://www.nceas.ucsb.edu 
> <http://www.nceas.ucsb.edu/>; http://arcticdata.io 
> <http://arcticdata.io/>; http://lternet.edu <http://lternet.edu/>
> NOTE CHANGE-- Ph: 805-886-9526  FAX: 805-893-7541
> 
> 
> 
> On Fri, Jul 13, 2018 at 2:50 PM John Graybeal via esip-semanticweb 
> <esip-semanticweb at lists.esipfed.org 
> <mailto:esip-semanticweb at lists.esipfed.org>> wrote:
> 
>     Hi Justin,
> 
>     Can you please share your previous assignment’s results with the
>     list? The community would be very interested in your conclusions,
>     especially after contributing to them!
> 
>     What would be especially powerful is that if you find vocabularies
>     that are *not* in any of the repositories mentioned below,
>     describing those to this community would let the repositories
>     encourage their submission. (Now *there* is a worthy community
>     project for the ESIP semantic community!)
> 
>     Just by search for ‘ECO’ I found the following in different
>     repositories. I haven’t looked into any of these but since you
>     hadn’t mentioned your process I thought I should double-check that
>     you are aware of them.  You should search not just on a few letters
>     in an ontology name as I did, but also individual terms that would
>     be represented in an ontology that you would like to use.
> 
>     At MMI ORR (http://mmisw.org) I see Ecological Mapping and
>     Ecological Roles and the Carbon Cycle, and (most relevant even if
>     oldest) a CMECS Habitat Classification Network vocabulary.
> 
>     Have you looked at BioPortal (http://bioportal.bioontology.org)? 
>     Entering ‘eco’ into the Find an ontology box yields Plant
>     Experimental Conditions Ontology and The Ecosystem Ontology (not ECO
>     of OBO).
> 
>     Going to AgroPortal (http://agroprotal.bioontology.org) finds also
>     Agroecology Knowledge Management ontology. I would expect more
>     ontologies here that are related to your interest.
> 
>     At the OBO Foundry (http://www.obofoundry.org) I see the Biological
>     Collections Ontology, ecocore (core ecological entities), and FOODON
>     (entities which bear a ‘food role).
> 
>     At Linked Open Vocabularies (http://lov.okfn.org/) I found various
>     hits searching for ecosys, ecolog, and ecozone (!). ‘Eco’ found so
>     many hits I wasn’t willing to search through them today.
> 
>     The LOD cloud I found nothing.
> 
>     I think the concepts expressed by Scott Peckham’s CSDMS to be
>     compelling, but it is not a composable model and may not be in any
>     repository.
> 
>     I expect EPA might have some relevant vocabularies as well.
> 
>     Also please consider that just because an ontology is not
>     immediately available does not mean you should exclude it from
>     consideration. Sometimes older ontologies become unavailable, but
>     might be exactly what you need, and they can be easily reconstituted
>     if a need exists (and should be for historical use anyway!).  For
>     example you can contact the OBO Foundry to ask if they know about ECO.
> 
>     I might suggest that if you send your semi-final lists to this list,
>     and support lists for the OBO Foundry, BIoPortal, and AgroPortal,
>     you may find a few more suggestions popping up from those communities.
> 
>     John
> 
> 
> 
> 
>     ---------------------------------------
>     John Graybeal
>     jbgraybeal at mindspring.com <mailto:jbgraybeal at mindspring.com>
>     650-450-1853
>     skype: graybealski
>     linkedin: http://www.linkedin.com/in/johngraybeal/
> 
>>     On Jul 12, 2018, at 07:44, Justin Goldstein - NOAA Affiliate via
>>     esip-semanticweb <esip-semanticweb at lists.esipfed.org
>>     <mailto:esip-semanticweb at lists.esipfed.org>> wrote:
>>
>>     Hi everyone,
>>       In Vol 111, Issue 7 of this list, I had inquired about "NOAA
>>     Ontologies" in order to assist with some vocabulary work
>>     associated with my job.  Thank you to all for great suggestions. 
>>     I have completed that part of my assignment but am now in need for
>>     ontologies that could be used to describe ecological processes,
>>     /the context being to look at terrestrial ecological processes
>>     that are measurable and quantifiable from space./
>>
>>        Basically, I'm looking for an ontology that contains and
>>     relates items such as trophic levels, food webs, Gross Primary
>>     production, aquatic biogeochemistry, nitrogen deposition,
>>     photosynthesis, etc.
>>
>>        I've done a lot of research.  The OBO Eco
>>     <http://www.obofoundry.org/ontology/ecocore.html> seems intriguing
>>     but navigating to the .owl file produces a 404 error.  Similarly,
>>     the PCO <https://code.google.com/archive/p/popcomm-ontology/> is
>>     now closed.  SWEET doesn't seem to have the granularity needed,
>>     and Darwin Core isn't quite what I'm looking for since it focuses
>>     more on geology/paleontology.  I didn't see much pertaining to the
>>     above terms in the ESIP COR.
>>
>>        The best I've found so far is this SeaDataNet ontology
>>     <http://vocab.nerc.ac.uk/collection/P03/current/> on the NERC
>>     Vocabulary Server.
>>
>>        Ideally, I'd really something that both fits the criteria
>>     described above and which is actively being updated and used so
>>     that I could justify the selection of the ontology.
>>
>>        Any ideas would be appreciated.
>>
>>        Thank you very much.
>>        Justin
>>     -- 
>>     ________________________
>>     Justin Goldstein, Ph.D.
>>     Observing Systems and Operations Analysis
>>     Technology, Planning and Integration for Observation (TPIO) Division;
>>     NOAA National Environmental Satellite, Data, and Information
>>     Service (NESDIS)
>>     Employed By Riverside Technology
>>
>>       * 1335 East-West Highway Room 5305
>>       * Silver Spring, MD 20910 USA
>>      *
>>
>>     (301) 427-2564
>>
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