[GloBI] Ontology of Biotic Interactions?

Thu Dec 20 16:07:27 CET 2018

Thanks Jorrit, Hi John, let me know if there is anything I can do to help

On Tue, Dec 18, 2018 at 5:56 PM John Oswald <j-oswald at tamu.edu> 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
>
> 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>
> <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
> *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
>
> m: 770.713.8531
>
>
>
>
>
>
>
> *From: *GloBI <globi-bounces at lists.gbif.org>
> <globi-bounces at lists.gbif.org> on behalf of John Oswald
> <j-oswald at tamu.edu> <j-oswald at tamu.edu>
> *Date: *Monday, November 19, 2018 at 9:18 PM
> *To: *"globi at lists.gbif.org" <globi at lists.gbif.org> <globi at lists.gbif.org>
> <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
>
> 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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>
> GloBI at lists.gbif.org
>
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>
>
>
> _______________________________________________
>
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>
> GloBI at lists.gbif.org
>
> 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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