[GloBI] Ontology of Biotic Interactions?
Jorrit Poelen
jhpoelen at xs4all.nl
Wed Dec 19 03:13:06 CET 2018
Hi John -
Just to clarify: the list I shared in tabular form is the most recent,
and full, list of biotic interaction terms as captured by the Relation
Ontology today. Biotic interaction terms are those that are categorized
as "biotically
interacts with" at http://purl.obolibrary.org/obo/RO_0002437 .
My previous comment ("I am sure the list is incomplete") was to merely
invite submissions for new terms if needed.
-jorrit
On 12/18/18 5:56 PM, John Oswald wrote:
>
> Hi Jorrit,
>
> See below…
>
> Hey John -
>
> I've shared your desire to get a table of interactions terms of the
> Relations Ontology (RO) with Chris Mungall, the maintainer of RO
> (cc-ed) via https://github.com/oborel/obo-relations/issues/295
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_oborel_obo-2Drelations_issues_295&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=dueHTDSXJypeq0FI5lQj-v8NXbzS4gf6JC039fe2nsw&e=>
> .
>
> ---Thanks for forwarding the request.
>
> Meanwhile, I've created a minimal table of RO interaction terms for
> you to consider:
>
> https://github.com/globalbioticinteractions/nomer/blob/master/nomer/src/test/resources/org/globalbioticinteractions/nomer/match/ro.tsv
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_nomer_blob_master_nomer_src_test_resources_org_globalbioticinteractions_nomer_match_ro.tsv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=bLOnkmZ-Oq5JmC7nW_pIrM2xdeQGi8klGvn-2QGHVpI&e=>
>
> or
>
> https://raw.githubusercontent.com/globalbioticinteractions/nomer/master/nomer/src/test/resources/org/globalbioticinteractions/nomer/match/ro.tsv
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__raw.githubusercontent.com_globalbioticinteractions_nomer_master_nomer_src_test_resources_org_globalbioticinteractions_nomer_match_ro.tsv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=1iHGLvubXqi0EY1ZO8BnnOrL_5o_D--oPUoq5lCjvgg&e=>
>
>
> ---Thanks for this. But, to a systematist with world interests, this
> is a bit like just having access to a list of the species from one
> country. In order to evaluate how I might incorporate text and
> identifiers from the RO into my data capture, management, and sharing
> activities, I need to see the whole list. With only a partial list I
> don’t know how complete or incomplete the term-set in the RO is, so
> can’t evaluate its potential utility as a starting point for efforts
> on my end.
>
> If you have suggestions on adding terms (I am sure the list is
> incomplete), please do share / document them via
> https://github.com/oborel/obo-relations#requesting-new-relations
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_oborel_obo-2Drelations-23requesting-2Dnew-2Drelations&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=ZHSYxVNjDBCwzzZDQGY_xeoPClMCs9V1r-wtXtfwHxc&e=>
> . If that is doesn't work for you, please feel free to share a list
> here and we can probably figure something out.
>
> ---As implied above, until I can see the complete list of terms it is
> not really possible to begin to assess what additions it might be
> useful to make to the existing set of relations.
>
> Cheers,
>
> John
>
> Hope this helps,
>
> -jorrit
>
> On 11/27/18 3:41 PM, Jorrit Poelen wrote:
>
> Hi John:
>
> Thanks for sharing the access database file. I was able to convert
> the file to tsv files without too much trouble and had a look at
> the examples you shared.
>
> I appreciate how you normalized the life stages and sex of the
> interacting things. also, the reverse interactions and the pairs
> help to more intuitively understand and parse the data.
>
> Re: associationTypes - When looking at the association kinds (from
> tblAssocKinds), I realized that bodyPart (e.g., "leaf"), life
> stage (e.g., "nymph") and physiological state (e.g., "dead") are
> mixed into the interaction type (e.g., "feeding on"). I can see
> how this notation can be handy for data entry or capture writing
> on labels, however, I would have the tendency to map the
> interaction phrases to separate the different kinds of things into
> separate columns, just like you did with lifestage and sex. That
> said, I'd always want to keep the verbatim interaction phrase
> around to preserve the original language.
>
> Re: list of OBO relations terms - they are listed, but in
> specialized formats (e.g., OBO, OWL) at
> http://purl.obolibrary.org/obo/ro.obo
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_ro.obo&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=UybvNHx81p3DwazHuzsD6wMSjnksyOfABjQORy-_URs&e=>
> and http://purl.obolibrary.org/obo/ro.owl
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_ro.owl&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=cyZaEdfpg8XRDTA_uT_M3JfJt9zDCJkuNSPHdJC0MI0&e=>
> respectively. I've opened an issue to remind myself to make it
> easier to provide a list (see
> <https://github.com/jhpoelen/eol-globi-data/issues/386>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jhpoelen_eol-2Dglobi-2Ddata_issues_386&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=S-CisqDftExwEZ8v8OLNYG8I8y_tPb5_E569M4nxEHs&e=>).
> For the time being, you might be inspired by a subset of the
> supported interactions types via
> <https://api.globalbioticinteractions.org/interactionTypes.csv?type=csv>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__api.globalbioticinteractions.org_interactionTypes.csv-3Ftype-3Dcsv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=WJRJNW0hGM_OJgBtvYFJn2LANpVTRuH4UGYiYwp9njg&e=>
> . More on that later.
>
> Re: mapping interaction terms - I agree that automated mapping is
> tricky business. What I had in mind is more of a static
> translation table that is used to maintain how one systems
> interaction terms (like yours) would translate into another naming
> scheme (like OBO Relations Ontology). In our case, an automation
> would use the static translation table to link the RO terms. So,
> no fancy methods here. An example of such a translation table can
> be found at
> https://github.com/globalbioticinteractions/inaturalist
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_inaturalist&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=vfFj0sH8Q1u7SHFS8fr_Ftlv2LVRY6SmVjDa1Jbrk6Q&e=>
> :
> https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types.csv
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_inaturalist_blob_master_interaction-5Ftypes.csv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=eK2zxDUlkmks2vwdBAQhS9LnfOo9bSLzkb4ZhGJa-No&e=>
> translates terms native the iNaturalist into RO .
> https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types_ignored.csv
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_inaturalist_blob_master_interaction-5Ftypes-5Fignored.csv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=dyHroS0Jg3VwKa2K2uvcKDjZgUIs8uOtl47tDSXLUH4&e=>
> contains a list of terms that are explicitly ignored.
>
> Re: next steps - in my experience, highly normalized data
> structures are important and useful when actively managing and
> curating data. However, when exporting data to other systems,
> often a denormalized format (aka "wide single table") really makes
> life a lot easier for moving snapshots of the data around . . . as
> long as it's automated and the identifiers are preserved. So, my
> suggested next step in our integration would be to figure out how
> to create a method that automatically generates a de-normalized
> table from your wealth of association data in a similar form as
> outlined in
> https://github.com/globalbioticinteractions/template-dataset
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_template-2Ddataset&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=2RaJvXtmF7EAnNl8f0B3GrpGykRYsndcs6P6Fr3hhfQ&e=>
> and, more specifically in
> https://github.com/globalbioticinteractions/template-dataset/blob/master/interactions.tsv
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_template-2Ddataset_blob_master_interactions.tsv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=Ryx7Z2SNz7Ar7p58vJU1A0qpkstpPLY0kpGzxLJytuo&e=>
> . Once the de-normalization is complete, terms (like assocKinds,
> but also lifestage, bodypart, physiological state) can be
> translated using static translation tables (see above).
>
> In short - in my view, an integration would preserve the autonomy
> of local data management, including terms, while automating a
> translation into a de-normalized format friendly for integration.
> This allows to updates to easily flow through the system without
> manual intervention without effecting the existing data management
> platform. Most importantly perhaps, the process contains
> sufficient information for GloBI (or others) to link back into
> your database as well as the original sources / specimen.
>
> I hope this helps and I'd be interested to help document this
> integration between your Neuropterida database with GloBI as a use
> case to share with our peers.
>
> Curious to hear your thoughts,
>
> -jorrit
>
> On 11/27/18 12:29 PM, John Oswald wrote:
>
> Hi Jorrit,
>
> See below…
>
> I think that sharing the Access database file would be a great
> start.
>
> ---I have just shared a Dropbox folder with you that contains
> an Access database that contains the several tables that I am
> currently working with to try to formulate a strategy for
> capturing relationship data. I’m happy to receive any
> comments/suggestions for improvements. The three tables are
> briefly discussed below.
>
> tblAssocKinds (association kinds) – Contains a list of 544
> “association kind” text strings. Many (ca. 200) of these
> originated with an initial 2010 dataset of associations that
> had been extracted from insect specimen labels by Norm Johnson
> of Ohio State University. I subsequently tried to standardize
> the phrasing of the original association strings, added
> additional strings, then tried to write “reverse association”
> strings so that there were pairs of phrases that could be used
> to state the relationship from the “opposite sides” of the
> association. The pairings are held in tblAssocPairs. Not all
> AssocKinds have reverse associations, so some are not
> currently included in a pair. The AssocKinds are mostly
> taxon-to-taxon or taxon-to-inanimate, but there are some
> outliers as I was experimenting with different kinds of
> associations. Is this kind of “reverse association”
> information useful in a broader context?
>
> tblAssocPairs (association pairs) – Contains pairings of
> values from tblAssocKinds.
>
> frmFlexAssocPairs – A simple query that contains AssocPairs as
> both AssocKind IDs and text strings (easier to read).
>
> tblAssociations – My current working table for capturing
> association data from the literature. This table currently
> contains only ca. 150 records of test data entered from the
> literature (I want to make sure that I get things set up
> optimally before extending the data capture effort). The table
> is general structured around a “left” associate and a “right”
> associate, “separated” by an AssocPair ID that links to
> tblAssocPairs. The table is currently structured for ease of
> data capture from the literature, and includes some other
> kinds of desirable data (e.g., sex, life stage, geography,
> literature source) that would be captured from the same
> literature sources. As I get into this though, it seems clear
> that many of those other data, which will not be available for
> all associations, should probably be removed to other
> relationally-linked tables in order to keep the data
> normalized. In the current structure the “left” associate is
> assumed to be an insect species of the superorder
> Neuropterida, which is specified by a “combination object” ID
> (field LeftNidaCombObjID). For data entry purposes this ID
> links to an episodically re-calculated lookup table of >20,000
> genus-group/species-group scientific name combinations
> (essentially a master lookup table of almost every
> Neuropterida combination that has ever been used in the
> literature). This “combination” ID can be used to link into
> most of the related taxonomic and nomenclatural data in my
> database. The link to the literature source is specified in
> field BibObjPageCiteID (Bibliographic Object Page Citation
> ID), which is an identifier that specifies a particular
> page/plate in the neuropterid literature (from which can be
> looked up all of the typical bibliographic information about
> the literature source, plus other data linked to individual
> literature pages, e.g., figures, chresonyms, and other
> annotations). This links to my bibliographic dataset of
> 17,000+ published works that contain information on the
> Neuropterida.
>
> I imagine that a first GloBI integration (or any other
> integration) would preserve the existing system and implement
> an automated translation or mapping procedures (e.g., scripts).
>
> ---To the extent possible I would prefer to not have to rely
> on automated translations, which are prone to interpretation
> errors (or maybe I’m misunderstanding what is automated
> here…). I would prefer to “oversplit” the associations that I
> use in my database, then re-group those associations into
> aggregate sets that correspond to other set(s) of association
> types used by other projects. This would give me more
> flexibility for defining associations that are useful for my
> purposes, and more control over how those associations are
> mapped when used in (potentially multiple) other contexts.
> We’re probably saying basically the same thing here, but I
> would like to retain the ability to control/influence the
> basic mapping of associations through relationships defined in
> my database.
>
> One of such procedures would include a mapping from your
> internal association types into another naming scheme such as
> OBO Relation Onology (http://obofoundry.org/ontology/ro.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__obofoundry.org_ontology_ro.html&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=SYaRVnY0jiGjyYGGuj4Lx0dPncmBZFAatHgtwJ-h4Uk&s=so-xkW80dqsEkKPNLOdRhe1JCD0nC8HQgpn-zKjmaDE&e=>):
> the closer the terms are in meaning, the easier the mapping is.
>
> ---Right, see above. How can I get a complete listing of the
> relation strings used in the Relation Ontology, their
> definitions (meanings), and their hierarchical organization? I
> don’t know how to do that. Is that something you can
> conveniently download, put into a table-based format, then
> send to me so that I can incorporate it into my database to
> experiment with?
>
> ---I expect that the relations in the Relation Ontology are
> fairly general. Is there another ontology (or some other
> source of relation terms) that deals more specifically (or at
> least includes) more specific relations that would pertain
> between insect taxa and either insect or non-insect taxa,
> and/or insect taxa and inanimate objects? That is something
> that I would find useful. Does something like that exist?
> Outside of the Relation Ontology, where do you source other
> kinds of relations? Or, how does one go about contributing to
> the development of a more specific ontology of relations that
> pertain to insects? Would that be a useful thing?
>
> With such a translation / mapping method in place, others can
> more easily find your data and you can more easily find
> similar projects. Then, hopefully, over time, we'll learn from
> each other in discussion forums, professional meetings or
> workshops and make it easier to share and capture these
> complex datasets.
>
> ---I’m interested to know if others have already developed
> well-defined sets of terms/phrases that describe
> relations/associations among insects and other organisms and
> inanimate objects. Can you make any recommendations for where
> I might look to find to find such sets of terms/phrases? Do
> any of the other projects involved in GloBI have such
> term/phrase sets that are available for examination?
>
> Perhaps we'll even settle on some best practices!
>
> So, yes, please send a (complete/partial) copy of your native
> database files or raw datasets, so I can get a sense of what
> your datasets looks like.
>
> ---You should have received an e-mail from Dropbox on this
> today, or will soon.
>
> Cheers,
>
> John
>
> Curious to hear your thoughts,
>
> -jorrit
>
> On 11/21/18 11:32 AM, John Oswald wrote:
>
> Hi Jorrit,
>
> Thanks for responding. Deborah Paul mentioned to me at the
> recent ESA meeting in Vancouver, BC, that GloBI would be
> one place that I should look, so I hoped to make contact
> with you by posting to the GloBI listserver. See more
> interleaved below…
>
> ---oo0oo---
>
> John D. Oswald
>
> Professor of Entomology
>
> Curator, Texas A&M University Insect Collection
>
> Department of Entomology
>
> Texas A&M University
>
> College Station, TX 77843-2475
>
> E-mail: j-oswald at tamu.edu <mailto:j-oswald at tamu.edu>
>
> Phone: 1-979-862-3507
>
> Lacewing Digital Library: http://lacewing.tamu.edu/
>
> Bibliography of the Neuropterida:
> http://lacewing.tamu.edu/Biblio/Main
>
> Neuropterida Species of the World:
> http://lacewing.tamu.edu/SpeciesCatalog/Main
>
> *From:*GloBI <globi-bounces at lists.gbif.org>
> <mailto:globi-bounces at lists.gbif.org>*On Behalf Of *Jorrit
> Poelen
> *Sent:* Tuesday, November 20, 2018 8:59 PM
> *To:* globi at lists.gbif.org <mailto:globi at lists.gbif.org>
> *Subject:* Re: [GloBI] Ontology of Biotic Interactions?
>
> Hey John -
>
> Like Robert (hi Robert!) mentioned, GloBI is also using
> the OBO Relations Ontology for defining biotic and abiotic
> interaction types, just like many other projects.
>
> ---As a newbie to ontologies (and an entomologist, not a
> computer scientist) I’m still trying to wrap my head
> around ontologies. In a nutshell, so far as I can
> determine, an ontology is at heart an extended web of
> controlled vocabulary terms with relationships defined
> between terms at different web nodes (terms), together
> with facilities to link to other ontologies. Is that about
> right?
>
> I've been attempting to collect my thoughts on data format
> and models at
> https://github.com/jhpoelen/globis-b-interactions/blob/master/text/on-species-interaction-data-models-and-formats.md
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jhpoelen_globis-2Db-2Dinteractions_blob_master_text_on-2Dspecies-2Dinteraction-2Ddata-2Dmodels-2Dand-2Dformats.md&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=RumeEb9OhO5-uPYMBvLVR_6mx3SCkPawDJ-uJYJWSC4&s=5rsVFs3GJwqHVhJgL9CJ3zhrFjEJuilAn7bu9SAW91c&e=>
> .
>
> ---Thanks for the link. I have briefly looked this over
> just now, but will go back for a detailed read later.
> There appears much there that would be good for me to
> consider as I continue development on my end.
>
> In my experience, an effective way to figure out how to
> capture/share your data is to use what you have today (as
> is!) and try to integrate a subset of it with other
> projects (like GloBI, GBIF).
>
> ---For the present, as briefly explained in my initial
> e-mail, I’m mostly trying to set up an efficient way to
> capture data on interactions/associations of neuropterid
> species with other taxa, inanimate objects, and concepts
> in my personal Neuropterida research database on the three
> insect orders Neuroptera, Megaloptera, and Raphidioptera.
> The Neuropterida database (currently built in Access) is
> highly parsed (ca. 350 relationally linked tables,
> including ca. 150 standardized ‘lookup’ tables covering
> various subjects), and significantly normalized (ca. 300
> tables normalized to 3NF or better). The core data are
> bibliographic, nomenclatural, taxonomic, and ‘agent
> based’, but there are extensions going off in many other
> directions. I currently share parts of these data via
> episodic downloads to support a variety of projects –
> particularly the Neuropterida domain of the Catalogue of
> Life (used by GBIF and many other projects globally), and
> the various modules of the Lacewing Digital Library
> project (lacewing.tamu.edu). I am an insect
> systematist/taxonomist by training, but I got into
> databasing in the early 1990’s and have been capturing
> data on the Neuropterida ever since. I am currently
> involved in a project whose primary product will be a new
> module in the Lacewing Digital Library that is devoted to
> interactions/associations (mostly predator/prey) of
> neuropterid insects and hemipterous insects. Thus, my
> primary motivation at the current time is to develop an
> effective and efficient database subschema for capturing
> these kinds of data, and to relationally link that
> subschema into my existing overall database schema. I
> would like to do this in a fairly general way so that I
> can (1) capture a wide variety of different kinds of
> interaction/association data into the same subschema of my
> database, (2) standardize the terminology/phrasing that I
> use so that terms/phrases are based on explicit
> definitions and are consistent with other similar
> controlled vocabularies for similar projects (to the
> extent that this may be possible; thus my foray here into
> ontologies…), and (3) be reasonably sure that there is
> fairly straightforward pathway through which whatever
> interaction/association subschema I develop within my
> database that it can be linked out to other projects that
> I might get involved with in the future.
>
> Your projects sounds very similar to other projects that
> have already been integrated into GloBI - a mix of
> specimen and literature data with their own way of
> describing interaction terms.
>
> ---Yes, I am sure that there are lots of other projects
> that are capturing similar data. I’d like to learn from
> those projects so that I can avoid any common pitfalls and
> ‘start off on the right foot’ as I get into this. To the
> extent possible, as I get started, I’d like to tap into
> any well-defined sets of interaction terms that may
> already exist. My initial though has been to build out
> this subschema in my database starting from my current
> table of ‘association kinds’. But I’m open to new ideas,
> and looking for someone who might be interested to discuss
> such issues.
>
> Do you have some samples that you can share so that I can
> get a sense of what you currently have?
>
> ---Sure. I can export a few tables to a simple Access
> database and send that to you. Can you work with that?
> Please confirm. If so, I can e-mail it to you or post it
> to you via Dropbox (depending on size).
>
> ---One of the difficulties that I am currently having is
> how one might extract the “data items” (to me this would
> be the set of controlled terms/phrases and their linking
> interaction/association terms) from one or more ontologies
> so that those data can be placed into and manipulated
> within a relational database structure. Is there an easy
> way to do that?
>
> Cheers,
>
> John
>
> thx,
>
> -jorrit
>
> https://globalbioticinteractions.org
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__globalbioticinteractions.org&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=RumeEb9OhO5-uPYMBvLVR_6mx3SCkPawDJ-uJYJWSC4&s=I3T9B7MwP8QsKCbpPfmjxbX37fWerqfnZPmO9RYlbCM&e=>
>
>
> On 11/19/18 6:21 PM, Bates, Robert P wrote:
>
> Hi John,
>
> We’ve been working with subsets of the OBO Relation
> Ontology (which if I’m not mistaken is also what GloBI
> uses) to provide the concepts for interaction
> relationships in our VERA modeling system:
>
> http://www.obofoundry.org/ontology/ro.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.obofoundry.org_ontology_ro.html&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=RumeEb9OhO5-uPYMBvLVR_6mx3SCkPawDJ-uJYJWSC4&s=kzb8EYNLqZjOBHOdXtKcwh141kUweLk_nINGFtUMVDc&e=>
>
> -R
>
> *Robert Bates*
>
> Research Scientist
>
> Design & Intelligence Lab
>
> *Georgia Institute of Technology*
>
> Technology Square Research Building, 85 5th Street NW,
> Atlanta, GA 30308
>
> e: rbates8 at gatech.edu <mailto:rbates8 at gatech.edu>
>
> m: 770.713.8531
>
> *From: *GloBI <globi-bounces at lists.gbif.org>
> <mailto:globi-bounces at lists.gbif.org>on behalf of John
> Oswald <j-oswald at tamu.edu> <mailto:j-oswald at tamu.edu>
> *Date: *Monday, November 19, 2018 at 9:18 PM
> *To: *"globi at lists.gbif.org"
> <mailto:globi at lists.gbif.org><globi at lists.gbif.org>
> <mailto:globi at lists.gbif.org>
> *Subject: *[GloBI] Ontology of Biotic Interactions?
>
> I’m growing and extending interaction/association data
> in my research database on the species of the
> superorder Neuropterida (Insecta: orders Neuroptera,
> Megaloptera, and Raphidioptera) of the world. The data
> is primarily drawn from the published literature; some
> also from specimen labels. I’m interested in
> standardizing the terminology that I use to describe
> interactions and associations. I’m interested in taxon
> to taxon interactions (e.g., species X eats species Y;
> species X is phoretic on species Y), taxon to
> inanimate object interactions/associations (e.g.,
> species X oviposits on substrate Y [say, rocks]), and
> taxon to concept associations (e.g., species X
> exhibits behavior Y). Can anyone recommend any good
> lists of standardized terms (with definitions) for
> this sort of thing? Are there any good, well
> developed, ontologies for general taxon-taxon and/or
> taxon-inanimate interactions? I have a list of 500+
> “association kinds” (without well-standardized
> definitions) that I have scraped together over the
> years. I’d like to plug these into (or convert them
> into) something more standardized if something more
> standard exists. Thanks for any suggestions on where I
> might go next on this.
>
> ---oo0oo---
>
> John D. Oswald
>
> Professor of Entomology
>
> Curator, Texas A&M University Insect Collection
>
> Department of Entomology
>
> Texas A&M University
>
> College Station, TX 77843-2475
>
> E-mail: j-oswald at tamu.edu <mailto:j-oswald at tamu.edu>
>
> Phone: 1-979-862-3507
>
> Lacewing Digital Library: http://lacewing.tamu.edu/
>
> Bibliography of the Neuropterida:
> http://lacewing.tamu.edu/Biblio/Main
>
> Neuropterida Species of the World:
> http://lacewing.tamu.edu/SpeciesCatalog/Main
>
>
>
>
>
> _______________________________________________
>
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>
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>
> https://lists.gbif.org/mailman/listinfo/globi <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.gbif.org_mailman_listinfo_globi&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=RumeEb9OhO5-uPYMBvLVR_6mx3SCkPawDJ-uJYJWSC4&s=RymsxaAO66KIoZRhT4qKmGNaLZuQhGlJY83ri2bvwfQ&e=>
>
>
>
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>
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>
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>
> https://lists.gbif.org/mailman/listinfo/globi <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.gbif.org_mailman_listinfo_globi&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=dq_dlLrMM9z2gJgcmJE1tsHmtykunazOcoxOEwhjV9o&e=>
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