<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>Hi John - <br>
</p>
<p>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<br>
interacts with" at <a class="moz-txt-link-freetext" href="http://purl.obolibrary.org/obo/RO_0002437">http://purl.obolibrary.org/obo/RO_0002437</a> .<br>
</p>
<p>My previous comment ("I am sure the list is incomplete") was to
merely invite submissions for new terms if needed.<br>
</p>
<p>-jorrit<br>
</p>
<div class="moz-cite-prefix">On 12/18/18 5:56 PM, John Oswald wrote:<br>
</div>
<blockquote type="cite"
cite="mid:f60a10ca4a5e4a1b947b93aa5203d2ad@tamu.edu">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="Generator" content="Microsoft Word 15 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
color:black;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;
color:black;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
color:black;}
span.EmailStyle21
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.EmailStyle22
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.EmailStyle23
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:#1F497D;}
span.EmailStyle24
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:#1F497D;}
span.EmailStyle25
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span style="color:red">Hi Jorrit,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:red"> See below…</span><span
style="color:red"><o:p></o:p></span></p>
<p>Hey John - <span style="font-size:12.0pt"><o:p></o:p></span></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
href="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="
moz-do-not-send="true">
https://github.com/oborel/obo-relations/issues/295</a> .<o:p></o:p></p>
<p><span style="color:red">---Thanks for forwarding the request.
<o:p></o:p></span></p>
<p>Meanwhile, I've created a minimal table of RO interaction
terms for you to consider:<o:p></o:p></p>
<p><a
href="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="
moz-do-not-send="true">https://github.com/globalbioticinteractions/nomer/blob/master/nomer/src/test/resources/org/globalbioticinteractions/nomer/match/ro.tsv</a><o:p></o:p></p>
<p>or<o:p></o:p></p>
<p><a
href="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="
moz-do-not-send="true">https://raw.githubusercontent.com/globalbioticinteractions/nomer/master/nomer/src/test/resources/org/globalbioticinteractions/nomer/match/ro.tsv</a>
<o:p></o:p></p>
<p><span style="color:red">---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.<o:p></o:p></span></p>
<p>If you have suggestions on adding terms (I am sure the list
is incomplete), please do share / document them via
<a
href="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="
moz-do-not-send="true">
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.<o:p></o:p></p>
<p><span style="color:red">---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.<o:p></o:p></span></p>
<p><span style="color:red">Cheers,<o:p></o:p></span></p>
<p><span style="color:red">John<o:p></o:p></span></p>
<p>Hope this helps,<o:p></o:p></p>
<p>-jorrit<o:p></o:p></p>
<div>
<p class="MsoNormal">On 11/27/18 3:41 PM, Jorrit Poelen wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p>Hi John:<o:p></o:p></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.<o:p></o:p></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.<o:p></o:p></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.<o:p></o:p></p>
<p>Re: list of OBO relations terms - they are listed, but in
specialized formats (e.g., OBO, OWL) at
<a
href="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="
moz-do-not-send="true">
http://purl.obolibrary.org/obo/ro.obo</a> and <a
href="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="
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
href="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="
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
href="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="
moz-do-not-send="true">
<https://api.globalbioticinteractions.org/interactionTypes.csv?type=csv></a>
. More on that later.<o:p></o:p></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
href="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="
moz-do-not-send="true">
https://github.com/globalbioticinteractions/inaturalist</a>
: <a
href="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="
moz-do-not-send="true">
https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types.csv</a>
translates terms native the iNaturalist into RO .
<a
href="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="
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.
<o:p></o:p></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
href="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="
moz-do-not-send="true">
https://github.com/globalbioticinteractions/template-dataset</a> and,
more specifically in
<a
href="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="
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). <o:p></o:p></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.
<o:p></o:p></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.<o:p></o:p></p>
<p>Curious to hear your thoughts,<o:p></o:p></p>
<p>-jorrit<o:p></o:p></p>
<p><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 11/27/18 12:29 PM, 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"> See
below…</span><o:p></o:p></p>
<p>I think that sharing the Access database file would be a
great start. <o:p></o:p></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.</span><o:p></o:p></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?</span><o:p></o:p></p>
<p><span style="color:#1F497D">tblAssocPairs (association
pairs) – Contains pairings of values from tblAssocKinds.</span><o:p></o:p></p>
<p><span style="color:#1F497D">frmFlexAssocPairs – A simple
query that contains AssocPairs as both AssocKind IDs and
text strings (easier to read).</span><o:p></o:p></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.</span><o:p></o:p></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.</span><o:p></o:p></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?</span><o:p></o:p></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.</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>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"><br>
<br>
<br>
<br>
</span><o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>GloBI mailing list<o:p></o:p></pre>
<pre><a href="mailto:GloBI@lists.gbif.org" moz-do-not-send="true">GloBI@lists.gbif.org</a><o:p></o:p></pre>
<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>
</blockquote>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif"><br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>GloBI mailing list<o:p></o:p></pre>
<pre><a href="mailto:GloBI@lists.gbif.org" moz-do-not-send="true">GloBI@lists.gbif.org</a><o:p></o:p></pre>
<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=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=dq_dlLrMM9z2gJgcmJE1tsHmtykunazOcoxOEwhjV9o&e=" moz-do-not-send="true">https://lists.gbif.org/mailman/listinfo/globi</a><o:p></o:p></pre>
</blockquote>
</div>
</blockquote>
</body>
</html>