{"id":100,"date":"2021-06-14T12:10:00","date_gmt":"2021-06-14T10:10:00","guid":{"rendered":"http:\/\/ntsafack.com\/?page_id=100"},"modified":"2021-06-14T12:10:01","modified_gmt":"2021-06-14T10:10:01","slug":"mouse-modular-ontology-for-unified-statistical-ecology","status":"publish","type":"page","link":"https:\/\/ntsafack.com\/index.php\/mouse-modular-ontology-for-unified-statistical-ecology\/","title":{"rendered":"MOUSE: Modular Ontology for Unified Statistical Ecology"},"content":{"rendered":"\n<p>I am developing, as a personal project, an ontology for classifying statistical results of ecological studies.<br>Ontologies are developed in the computing and biomedial domains, but the subject in still young in the ecology field.<br>My project aims to provide a toolkit, for ecologists, for classifying their results (field and lab data, statistical analyses).<br>This new ontology will be tailored to the needs of the field of ecology and will rely heavily on existing ontologies, some developed for other domains.<\/p>\n\n\n\n<p>&nbsp;&nbsp;<a href=\"https:\/\/github.com\/noetsa\/Mouses\">https:\/\/github.com\/noetsa\/Mouses<\/a><\/p>\n\n\n\n<h3>&nbsp;<\/h3>\n\n\n\n<h3>Goals<\/h3>\n\n\n\n<ul><li>Provide a toolkit for classifying ecology results and studies<\/li><li>Facilitate comparison between studies<\/li><li>Facilitate queries on existing studies<\/li><li>Make meta-studies easier<\/li><li>Facilitate input preparation for future Machine Learning\/Artificial Intelligence studies.<\/li><\/ul>\n\n\n\n<h3>&nbsp;<\/h3>\n\n\n\n<h3>Properties<\/h3>\n\n\n\n<p>This new ontology should have these desirable properties (non-exhaustive list):<\/p>\n\n\n\n<ul><li>Relies mostly on imported concepts from existing, established ontologies.<\/li><li>Interoperates well with these existing ontologies.<\/li><li>Eliminates or minimizes redundancy of concepts imported from other ontologies.<\/li><li>Uses BFO, the Basic Formal Ontology, for consistency with many existing scientific ontologies.<\/li><li>Includes most common concepts used in ecology and in ecological studies and results.<\/li><li>Statistical methods are hierarchically organized and have properties. This enables comparison between statistical methods.<\/li><li>When possible relations between statistical methods\/results are defined. For example, can we define the &#8220;total variance&#8221; of two statistical results?&nbsp;<\/li><li>Environments, species are also imported or accessible from the ontology.<\/li><li>Ideally, when the ontology is complete and a good number of ecological studies are defined using the ontology, queries such as the following could be answered by a reasoner: &#8220;mean population of diptera in arid climate, years between 1990 and 2005, with number and name of studies, and combined error measure&#8221;<\/li><\/ul>\n\n\n\n<p>Some of these goals may be mutually exclusive so sometimes it will be a matter of balance. If a community develops around this project, feedback will be very valuable to achieve balance between competing desirable properties.<\/p>\n\n\n\n<h4>&nbsp;<\/h4>\n\n\n\n<h4>Imported ontologies<\/h4>\n\n\n\n<p>STATO (currently in full)&nbsp;<a href=\"https:\/\/bioportal.bioontology.org\/ontologies\/STATO\">https:\/\/bioportal.bioontology.org\/ontologies\/STATO<\/a><br>MAMO (excluding domain specific classes)&nbsp;<a href=\"https:\/\/sourceforge.net\/projects\/mamo-ontology\/\">https:\/\/sourceforge.net\/projects\/mamo-ontology\/<\/a><br>OBOE (currently in full)&nbsp;<a href=\"https:\/\/github.com\/NCEAS\/oboe\/\">https:\/\/github.com\/NCEAS\/oboe\/<\/a><\/p>\n\n\n\n<h4>&nbsp;<\/h4>\n\n\n\n<h4>Considered ontologies for future import, compliance or interaction<\/h4>\n\n\n\n<p>BFO&nbsp;<a href=\"https:\/\/github.com\/BFO-ontology\/BFO\">https:\/\/github.com\/BFO-ontology\/BFO<\/a><br>NCBITaxon&nbsp;<a href=\"http:\/\/www.obofoundry.org\/ontology\/ncbitaxon.html\">http:\/\/www.obofoundry.org\/ontology\/ncbitaxon.html<\/a><br>Other ontologies to consider: Ontologies about GIS, containing concepts such as point, coordinates, area, area shape, area size, fragmentation, width, neighboring, distance, etc.<\/p>\n\n\n\n<h4>&nbsp;<\/h4>\n\n\n\n<h4>Ontologies of interest, not imported at the moment<\/h4>\n\n\n\n<p>ENVO&nbsp;<a href=\"https:\/\/bioportal.bioontology.org\/ontologies\/ENVO\">https:\/\/bioportal.bioontology.org\/ontologies\/ENVO<\/a><br>BCO&nbsp;<a href=\"https:\/\/bioportal.bioontology.org\/ontologies\/BCO\">https:\/\/bioportal.bioontology.org\/ontologies\/BCO<\/a><br>PCO&nbsp;<a href=\"https:\/\/bioportal.bioontology.org\/ontologies\/PCO\">https:\/\/bioportal.bioontology.org\/ontologies\/PCO<\/a><br>Agronomy Ontology&nbsp;<a href=\"https:\/\/github.com\/AgriculturalSemantics\/agro\">https:\/\/github.com\/AgriculturalSemantics\/agro<\/a><br>ecocore&nbsp;<a href=\"https:\/\/github.com\/EcologicalSemantics\/ecocore\">https:\/\/github.com\/EcologicalSemantics\/ecocore<\/a><br>SWEET&nbsp;<a href=\"https:\/\/github.com\/ESIPFed\/sweet\">https:\/\/github.com\/ESIPFed\/sweet<\/a><\/p>\n\n\n\n<h4>Other ontologies<\/h4>\n\n\n\n<p>OBCS&nbsp;<a href=\"https:\/\/github.com\/obcs\/obcs\">https:\/\/github.com\/obcs\/obcs<\/a><br>EDAM&nbsp;<a href=\"http:\/\/edamontology.org\/page\">http:\/\/edamontology.org\/page<\/a><br>GEOSPECIES&nbsp;<a href=\"https:\/\/bioportal.bioontology.org\/ontologies\/GEOSPECIES\">https:\/\/bioportal.bioontology.org\/ontologies\/GEOSPECIES<\/a><\/p>\n\n\n\n<h3>&nbsp;<\/h3>\n\n\n\n<h3>&nbsp;<\/h3>\n\n\n\n<h3>Plan<\/h3>\n\n\n\n<p>Version 0.1:<br>-Organize imported concepts of STATO, MAMO and OBOE ontologies within the new ontology, while considering compatibility with BFO ontology.<br>-Work out licencing and citation mechanisms for both imported and new ontology<br>-Publish version 0.1 of MOUSE ontology on GitHub<\/p>\n\n\n\n<p>Version 0.2:<br>-Import needed concepts of ENVO, BCO, PCO, Agronomy Ontology, ecocore, SWEET ontologies, and GIS concepts ontology.<\/p>\n\n\n\n<p>Version 0.3:<br>-Import\/interface with NCBITaxon ontology, or the NCBI Taxon database.<\/p>\n\n\n\n<p>Version 0.4:<br>-Create missing concepts for our domain. Test basic queries.<\/p>\n\n\n\n<p>Version 0.5:<br>-Work on the relationships between statistical results.<\/p>\n\n\n\n<p>If you have insights on the subject, know of relevant or similar ontologies, work on a similar project, or wish to share ideas, please contact me \ud83d\ude42<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I am developing, as a personal project, an ontology for classifying statistical results of ecological studies.Ontologies are developed in the computing and biomedial domains, but &hellip;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/ntsafack.com\/index.php\/wp-json\/wp\/v2\/pages\/100"}],"collection":[{"href":"https:\/\/ntsafack.com\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ntsafack.com\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ntsafack.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ntsafack.com\/index.php\/wp-json\/wp\/v2\/comments?post=100"}],"version-history":[{"count":1,"href":"https:\/\/ntsafack.com\/index.php\/wp-json\/wp\/v2\/pages\/100\/revisions"}],"predecessor-version":[{"id":101,"href":"https:\/\/ntsafack.com\/index.php\/wp-json\/wp\/v2\/pages\/100\/revisions\/101"}],"wp:attachment":[{"href":"https:\/\/ntsafack.com\/index.php\/wp-json\/wp\/v2\/media?parent=100"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}