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<p>Hey John - <br>
</p>
<p>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 <a class="moz-txt-link-freetext" href="https://github.com/oborel/obo-relations/issues/295">https://github.com/oborel/obo-relations/issues/295</a>
.</p>
<p>Meanwhile, I've created a minimal table of RO interaction terms
for you to consider:</p>
<p><a class="moz-txt-link-freetext" href="https://github.com/globalbioticinteractions/nomer/blob/master/nomer/src/test/resources/org/globalbioticinteractions/nomer/match/ro.tsv">https://github.com/globalbioticinteractions/nomer/blob/master/nomer/src/test/resources/org/globalbioticinteractions/nomer/match/ro.tsv</a></p>
<p>or</p>
<p><a class="moz-txt-link-freetext" href="https://raw.githubusercontent.com/globalbioticinteractions/nomer/master/nomer/src/test/resources/org/globalbioticinteractions/nomer/match/ro.tsv">https://raw.githubusercontent.com/globalbioticinteractions/nomer/master/nomer/src/test/resources/org/globalbioticinteractions/nomer/match/ro.tsv</a>
<br>
</p>
<p>If you have suggestions on adding terms (I am sure the list is
incomplete), please do share / document them via
<a class="moz-txt-link-freetext" href="https://github.com/oborel/obo-relations#requesting-new-relations">https://github.com/oborel/obo-relations#requesting-new-relations</a> .
If that is doesn't work for you, please feel free to share a list
here and we can probably figure something out.</p>
<p>Hope this helps,</p>
<p>-jorrit<br>
</p>
<div class="moz-cite-prefix">On 11/27/18 3:41 PM, Jorrit Poelen
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:612d4042-61dc-3eca-8ba3-3d1c5fb253da@xs4all.nl">
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<p>Hi John:</p>
<p>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.<br>
</p>
<p>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.<br>
</p>
<p>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.<br>
</p>
<p>Re: list of OBO relations terms - they are listed, but in
specialized formats (e.g., OBO, OWL) at <a
class="moz-txt-link-freetext"
href="http://purl.obolibrary.org/obo/ro.obo"
moz-do-not-send="true">http://purl.obolibrary.org/obo/ro.obo</a>
and <a class="moz-txt-link-freetext"
href="http://purl.obolibrary.org/obo/ro.owl"
moz-do-not-send="true">http://purl.obolibrary.org/obo/ro.owl</a>
respectively. I've opened an issue to remind myself to make it
easier to provide a list (see <a class="moz-txt-link-rfc2396E"
href="https://github.com/jhpoelen/eol-globi-data/issues/386"
moz-do-not-send="true"><https://github.com/jhpoelen/eol-globi-data/issues/386></a>).
For the time being, you might be inspired by a subset of the
supported interactions types via
<a class="moz-txt-link-rfc2396E"
href="https://api.globalbioticinteractions.org/interactionTypes.csv?type=csv"
moz-do-not-send="true"><https://api.globalbioticinteractions.org/interactionTypes.csv?type=csv></a>
. More on that later.</p>
<p>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 <a
class="moz-txt-link-freetext"
href="https://github.com/globalbioticinteractions/inaturalist"
moz-do-not-send="true">https://github.com/globalbioticinteractions/inaturalist</a>
:
<a class="moz-txt-link-freetext"
href="https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types.csv"
moz-do-not-send="true">https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types.csv</a>
translates terms native the iNaturalist into RO .
<a class="moz-txt-link-freetext"
href="https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types_ignored.csv"
moz-do-not-send="true">https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types_ignored.csv</a>
contains a list of terms that are explicitly ignored. <br>
</p>
<p>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 <a
class="moz-txt-link-freetext"
href="https://github.com/globalbioticinteractions/template-dataset"
moz-do-not-send="true">https://github.com/globalbioticinteractions/template-dataset</a>
and, more specifically in
<a class="moz-txt-link-freetext"
href="https://github.com/globalbioticinteractions/template-dataset/blob/master/interactions.tsv"
moz-do-not-send="true">https://github.com/globalbioticinteractions/template-dataset/blob/master/interactions.tsv</a>
. Once the de-normalization is complete, terms (like assocKinds,
but also lifestage, bodypart, physiological state) can be
translated using static translation tables (see above). <br>
</p>
<p>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. <br>
</p>
<p>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.<br>
</p>
<p>Curious to hear your thoughts,</p>
<p>-jorrit<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 11/27/18 12:29 PM, John Oswald
wrote:<br>
</div>
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<p class="MsoNormal"><span style="color:#1F497D">Hi Jorrit,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> See
below…<o:p></o:p></span></p>
<p>I think that sharing the Access database file would be a
great start. <span style="color:#1F497D"> <o:p></o:p></span></p>
<p><span style="color:#1F497D">---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.<o:p></o:p></span></p>
<p><span style="color:#1F497D">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?<o:p></o:p></span></p>
<p><span style="color:#1F497D">tblAssocPairs (association
pairs) – Contains pairings of values from tblAssocKinds.<o:p></o:p></span></p>
<p><span style="color:#1F497D">frmFlexAssocPairs – A simple
query that contains AssocPairs as both AssocKind IDs and
text strings (easier to read).<o:p></o:p></span></p>
<p><span style="color:#1F497D">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.<o:p></o:p></span></p>
<p>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). <o:p></o:p></p>
<p><span style="color:#1F497D">---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.<o:p></o:p></span></p>
<p>One of such procedures would include a mapping from your
internal association types into another naming scheme such
as OBO Relation Onology (<a
href="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="
moz-do-not-send="true">http://obofoundry.org/ontology/ro.html</a>):
the closer the terms are in meaning, the easier the mapping
is. <o:p></o:p></p>
<p><span style="color:#1F497D">---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?<o:p></o:p></span></p>
<p><span style="color:#1F497D">---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?</span><o:p></o:p></p>
<p>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. <o:p></o:p></p>
<p><span style="color:#1F497D">---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?</span><o:p></o:p></p>
<p>Perhaps we'll even settle on some best practices!<o:p></o:p></p>
<p>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. <o:p></o:p></p>
<p><span style="color:#1F497D">---You should have received an
e-mail from Dropbox on this today, or will soon.<o:p></o:p></span></p>
<p><span style="color:#1F497D">Cheers,<o:p></o:p></span></p>
<p><span style="color:#1F497D">John</span><o:p></o:p></p>
<p>Curious to hear your thoughts,<o:p></o:p></p>
<p>-jorrit<o:p></o:p></p>
<div>
<p class="MsoNormal">On 11/21/18 11:32 AM, John Oswald
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="color:#1F497D">Hi Jorrit,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> 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…</span><o:p></o:p></p>
<div>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">---oo0oo---</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">John D.
Oswald</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Professor
of Entomology</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Curator,
Texas A&M University Insect Collection</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Department
of Entomology</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Texas
A&M University</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">College
Station, TX 77843-2475</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">E-mail: </span><a
href="mailto:j-oswald@tamu.edu" moz-do-not-send="true"><span
style="color:blue">j-oswald@tamu.edu</span></a><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Phone:
1-979-862-3507</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Lacewing
Digital Library: </span> <a
href="http://lacewing.tamu.edu/"
moz-do-not-send="true"><span style="color:blue">http://lacewing.tamu.edu/</span></a><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Bibliography
of the Neuropterida: </span><a
href="http://lacewing.tamu.edu/Biblio/Main"
moz-do-not-send="true"><span style="color:blue">http://lacewing.tamu.edu/Biblio/Main</span></a><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Neuropterida
Species of the World: </span><a
href="http://lacewing.tamu.edu/SpeciesCatalog/Main"
moz-do-not-send="true"><span style="color:blue">http://lacewing.tamu.edu/SpeciesCatalog/Main</span></a><o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1

1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="color:windowtext">From:</span></b><span
style="color:windowtext"> GloBI </span><a
href="mailto:globi-bounces@lists.gbif.org"
moz-do-not-send="true"><globi-bounces@lists.gbif.org></a><span
style="color:windowtext"> <b>On Behalf Of </b>Jorrit
Poelen<br>
<b>Sent:</b> Tuesday, November 20, 2018 8:59 PM<br>
<b>To:</b> </span><a
href="mailto:globi@lists.gbif.org"
moz-do-not-send="true">globi@lists.gbif.org</a><span
style="color:windowtext"><br>
<b>Subject:</b> Re: [GloBI] Ontology of Biotic
Interactions?</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p>Hey John - <o:p></o:p></p>
<p>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. <o:p></o:p></p>
<p><span style="color:#1F497D">---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?</span><o:p></o:p></p>
<p>I've been attempting to collect my thoughts on data
format and models at <a
href="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="
moz-do-not-send="true">
https://github.com/jhpoelen/globis-b-interactions/blob/master/text/on-species-interaction-data-models-and-formats.md</a>
. <o:p></o:p></p>
<p><span style="color:#1F497D">---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.</span><o:p></o:p></p>
<p>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). <o:p></o:p></p>
<p><span style="color:#1F497D">---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.</span><o:p></o:p></p>
<p>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. <o:p></o:p></p>
<p><span style="color:#1F497D">---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.</span><o:p></o:p></p>
<p>Do you have some samples that you can share so that I can
get a sense of what you currently have? <o:p></o:p></p>
<p><span style="color:#1F497D">---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).</span><o:p></o:p></p>
<p><span style="color:#1F497D">---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?</span><o:p></o:p></p>
<p><span style="color:#1F497D">Cheers,</span><o:p></o:p></p>
<p><span style="color:#1F497D">John</span><o:p></o:p></p>
<p>thx,<o:p></o:p></p>
<p>-jorrit<o:p></o:p></p>
<p><a
href="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="
moz-do-not-send="true">https://globalbioticinteractions.org</a>
<o:p></o:p></p>
<div>
<p class="MsoNormal">On 11/19/18 6:21 PM, Bates, Robert P
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi John,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><a
href="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="
moz-do-not-send="true">http://www.obofoundry.org/ontology/ro.html</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">-R<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal"><b><span style="font-size:14.0pt">Robert
Bates</span></b><o:p></o:p></p>
<p class="MsoNormal">Research Scientist<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Design & Intelligence Lab<o:p></o:p></p>
<p class="MsoNormal"><b>Georgia Institute of Technology</b><o:p></o:p></p>
<p class="MsoNormal">Technology Square Research
Building, 85 5th Street NW, Atlanta, GA 30308<o:p></o:p></p>
<p class="MsoNormal">e: <a
href="mailto:rbates8@gatech.edu"
moz-do-not-send="true"><span style="color:purple">rbates8@gatech.edu</span></a><o:p></o:p></p>
<p class="MsoNormal">m: 770.713.8531<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF

1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt">From:
</span></b><span style="font-size:12.0pt">GloBI </span><a
href="mailto:globi-bounces@lists.gbif.org"
moz-do-not-send="true"><span
style="font-size:12.0pt"><globi-bounces@lists.gbif.org></span></a><span
style="font-size:12.0pt"> on behalf of John Oswald </span><a
href="mailto:j-oswald@tamu.edu"
moz-do-not-send="true"><span
style="font-size:12.0pt"><j-oswald@tamu.edu></span></a><span
style="font-size:12.0pt"><br>
<b>Date: </b>Monday, November 19, 2018 at 9:18 PM<br>
<b>To: </b></span><a
href="mailto:globi@lists.gbif.org"
moz-do-not-send="true"><span
style="font-size:12.0pt">"globi@lists.gbif.org"</span></a><span
style="font-size:12.0pt"> </span><a
href="mailto:globi@lists.gbif.org"
moz-do-not-send="true"><span
style="font-size:12.0pt"><globi@lists.gbif.org></span></a><span
style="font-size:12.0pt"><br>
<b>Subject: </b>[GloBI] Ontology of Biotic
Interactions?</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">---oo0oo---<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">John D. Oswald<o:p></o:p></p>
<p class="MsoNormal">Professor of Entomology<o:p></o:p></p>
<p class="MsoNormal">Curator, Texas A&M University
Insect Collection<o:p></o:p></p>
<p class="MsoNormal">Department of Entomology<o:p></o:p></p>
<p class="MsoNormal">Texas A&M University<o:p></o:p></p>
<p class="MsoNormal">College Station, TX 77843-2475<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">E-mail: <a
href="mailto:j-oswald@tamu.edu" moz-do-not-send="true"><span
style="color:blue">j-oswald@tamu.edu</span></a><o:p></o:p></p>
<p class="MsoNormal">Phone: 1-979-862-3507<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Lacewing Digital Library: <a
href="http://lacewing.tamu.edu/"
moz-do-not-send="true"> <span style="color:blue">http://lacewing.tamu.edu/</span></a><o:p></o:p></p>
<p class="MsoNormal">Bibliography of the Neuropterida: <a
href="http://lacewing.tamu.edu/Biblio/Main"
moz-do-not-send="true"> <span style="color:blue">http://lacewing.tamu.edu/Biblio/Main</span></a><o:p></o:p></p>
<p class="MsoNormal">Neuropterida Species of the World: <a
href="http://lacewing.tamu.edu/SpeciesCatalog/Main"
moz-do-not-send="true"> <span style="color:blue">http://lacewing.tamu.edu/SpeciesCatalog/Main</span></a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times
New
 Roman ,serif",serif"><br>
<br>
<br>
</span><o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>GloBI mailing list<o:p></o:p></pre>
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<pre><a href="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=" moz-do-not-send="true">https://lists.gbif.org/mailman/listinfo/globi</a><o:p></o:p></pre>
</blockquote>
</blockquote>
</div>
</blockquote>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
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