{"id":3057,"date":"2017-07-14T20:53:03","date_gmt":"2017-07-14T20:53:03","guid":{"rendered":"https:\/\/notebooks.dataone.org\/?p=3057"},"modified":"2019-05-24T17:37:08","modified_gmt":"2019-05-24T17:37:08","slug":"week-7-ecso-imports-old-and-new","status":"publish","type":"post","link":"https:\/\/notebooks.dataone.org\/controlled-vocab\/week-7-ecso-imports-old-and-new\/","title":{"rendered":"Week 7: ECSO Imports Old and New"},"content":{"rendered":"<p>This week I have been mainly focused on resolving issues with MIREOT imports. I checked all external import ontologies classes versus those within ECSO and found that on my Prot\u00e9g\u00e9 these were importing correctly. However, following a screen share yesterday with Margaret we discovered that she is missing external ontology import classes for example the ENVO_import.owl file has 1812 classes and ECSO should have 1812 ENVO classes but Margaret\u2019s ECSO only has 1634. All of the MIREOT imports that are having issues share the URL <a href=\"http:\/\/purl.dataone.org\">http:\/\/purl.dataone.org<\/a> while external ontologies hosted at other sites are not having any problems importing from the URL. For now we can load the owl import files directly from our local directories but this mystery continues to be an unresolved.<\/p>\n<p>This week I spent time duplicating all of the rdfs labels into hidden label for each term with ECSO. This is a very time consuming process but hopefully it will be done soon!<\/p>\n<p>Since this task is repetitive I have been breaking up the monotony with locating existing ontology class for the hundred some words that I had identified as needing to be added to ECSO. Many of these terms have been added to ENVO since the last ENVO_import.owl file was created and so I created a <a href=\"https:\/\/github.com\/DataONEorg\/sem-prov-ontologies\/blob\/ArcticECSO\/envo_imports2.owl\">new ENVO import <\/a>using the OntoFox web site. A few examples of new ENVO terms in this file include:<\/p>\n<p><strong>frazil ice<\/strong> \u2013 new ice which is composed of small, needle-like crystals consisting of nearly pure fresh water<\/p>\n<p><strong>thermokarst<\/strong> \u2013 an irregular land surface which consists of marshy hollows, hummocks, thermokarst depressions and the thermokarst lakes formed from the erosion of ice-rich thawing permafrost areas<\/p>\n<p><strong>polar tree-line ecotone<\/strong> \u2013 an ecotone which bridges a subpolar coniferous forest biome and a tundra biome<\/p>\n<p>Other imports from CHEBI also need to be added such as oxygen isotopes 16, 17 and 18, clumped isotopes, and compound specific isotopes since all of these data types are available through the Arctic Data Center. Anticipated data terminology need to be added as well for example carbonyl sulfide or COS which can be used to track CO2 uptake during plant photosynthesis you can read more about this new proxy <a href=\"http:\/\/www.nature.com\/ngeo\/journal\/v6\/n3\/abs\/ngeo1730.html\">here<\/a>.<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This week I have been mainly focused on resolving issues with MIREOT imports. I checked all external import ontologies classes versus those within ECSO and found that on my Prot\u00e9g\u00e9 these were importing correctly. However, following a screen share yesterday with Margaret we discovered that she is missing external ontology <a class=\"more-link\" href=\"https:\/\/notebooks.dataone.org\/controlled-vocab\/week-7-ecso-imports-old-and-new\/\">Continue reading <span class=\"screen-reader-text\">  Week 7: ECSO Imports Old and New<\/span><span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":106,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[376],"tags":[],"_links":{"self":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/3057"}],"collection":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/users\/106"}],"replies":[{"embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/comments?post=3057"}],"version-history":[{"count":1,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/3057\/revisions"}],"predecessor-version":[{"id":3058,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/3057\/revisions\/3058"}],"wp:attachment":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/media?parent=3057"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/categories?post=3057"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/tags?post=3057"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}