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<?xml version="1.0" encoding="UTF-8"?><rss version="2.0" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:wfw="http://wellformedweb.org/CommentAPI/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:atom="http://www.w3.org/2005/Atom" xmlns:sy="http://purl.org/rss/1.0/modules/syndication/" xmlns:slash="http://purl.org/rss/1.0/modules/slash/" > <channel> <title>BioPortal</title> <atom:link href="https://www.bioontology.org/feed/" rel="self" type="application/rss+xml" /> <link>https://www.bioontology.org</link> <description>Biomedical Ontology Repository</description> <lastBuildDate>Wed, 30 Sep 2020 15:02:36 +0000</lastBuildDate> <language>en-US</language> <sy:updatePeriod> hourly </sy:updatePeriod> <sy:updateFrequency> 1 </sy:updateFrequency> <generator>https://wordpress.org/?v=6.7.2</generator> <item> <title>Why BioPortal No Longer Offers the Current Procedural Terminology (CPT)</title> <link>https://www.bioontology.org/why-bioportal-no-longer-offers-the-current-procedural-terminology-cpt/</link> <dc:creator><![CDATA[John Graybeal]]></dc:creator> <pubDate>Wed, 30 Sep 2020 14:59:44 +0000</pubDate> <category><![CDATA[News]]></category> <guid isPermaLink="false">https://www.bioontology.org/?p=806</guid> <description><![CDATA[Hello everyone, I am sorry to be writing this post to explain why the Current Procedural Terminology (CPT) is no longer being served by BioPortal. We understand that this is a very important database, and we tried to convince its providers [1] to let BioPortal continue to serve it. Unfortunately, the owners of CPT make […]]]></description> <content:encoded><![CDATA[ Hello everyone, I am sorry to be writing this post to explain why the Current Procedural Terminology (CPT) is no longer being served by BioPortal. We understand that this is a very important database, and we tried to convince its providers [1] to let BioPortal continue to serve it. Unfortunately, the owners of CPT make their money to support development of their product by charging people to use it, and these owners determined that the way BioPortal was serving it was not consistent with the intent of their license. So the CPT owners requested that we take it down, and we agreed to their request. We would be happy to install it again if the owners of the license ever allow that again. Many of you have asked about alternatives to the CPT ontology that we served. To our knowledge, no one else serves CPT in the way we did (there is nothing else quite like BioPortal!). Even if someone does serve this content publicly, it seems likely that they, too, would be asked to remove it. However, there is a path by which you can access CPT separately, and even install it on your own private OntoPortal Appliance. Some technical competence and time is required to do this, but it’s possible. The following procedure also works for other UMLS ontologies that we have in BioPortal, but do not offer as downloads. individuals can download UMLS themselves using their own UMLS license [2]. Once you have obtained your license and downloaded the UMLS database, you can use the umls2rdf conversion software [3] to create the data in ontology form. This converted data can then be uploaded into your own OntoPortal repository [4]. If you are a REDCap user, you can consult with REDCap [5] about modifying the system to point to your OntoPortal deployment, instead of the BioPortal repository.) Of course all such uses must remain in accordance with the UMLS and CPT licenses under which the information is distributed. We encourage you to contact the CPT organization [1] to learn more about their licensing system. You may also wish to convey to them the value of public access to their critical data, although we are entirely sympathetic to their need to maintain a sustainable platform. Thank you for your support of the BioPortal and OntoPortal repositories and software. The BioPortal Team Stanford Center for Biomedical Informatics <ol class="wp-block-list"><li>Current Procedural Terminology: <a href="https://www.ama-assn.org/amaone/cpt-current-procedural-terminology">https://www.ama-assn.org/amaone/cpt-current-procedural-terminology</a></li><li>UMLS access and license: <a class="" href="https://www.nlm.nih.gov/databases/umls.html">https://www.nlm.nih.gov/databases/umls.html</a> </li><li>umls2rdf: <a class="" href="https://github.com/ncbo/umls2rdf">https://github.com/ncbo/umls2rdf</a></li><li>OntoPortal: <a class="" href="https://ontoportal.github.io/administration">https://ontoportal.github.io/administration</a></li><li>REDCap: <a href="https://www.project-redcap.org/">https://www.project-redcap.org/</a></li></ol> ]]></content:encoded> </item> <item> <title>BioPortal part of GO FAIR Foundation’s M4M Workshop</title> <link>https://www.bioontology.org/bioportal-part-of-go-fair-foundations-m4m-workshop/</link> <dc:creator><![CDATA[John Graybeal]]></dc:creator> <pubDate>Sat, 01 Aug 2020 04:42:08 +0000</pubDate> <category><![CDATA[Application Stories]]></category> <category><![CDATA[Applications]]></category> <category><![CDATA[Events]]></category> <category><![CDATA[Happenings]]></category> <category><![CDATA[CEDAR]]></category> <category><![CDATA[DeiC]]></category> <category><![CDATA[GO FAIR]]></category> <category><![CDATA[M4M Workshop]]></category> <guid isPermaLink="false">https://www.bioontology.org/?p=797</guid> <description><![CDATA[The GO FAIR Foundation has begun workshops #5 and #6 in a series of GO FAIR M4M Workshops, which aim to “Assess the state of metadata practices in the various scientific communities, look for improvements of the current fragmentation and promote good FAIR compliant practices.” For these particular workshops, applications from Stanford’s Center for BioMedical […]]]></description> <content:encoded><![CDATA[ The GO FAIR Foundation has begun workshops #5 and #6 in a series of <a rel="noreferrer noopener" href="https://www.go-fair.org/resources/go-fair-workshop-series/metadata-for-machines-workshops/" target="_blank">GO FAIR M4M Workshops</a>, which aim to “Assess the state of metadata practices in the various scientific communities, look for improvements of the current fragmentation and promote good FAIR compliant practices.” For these particular workshops, applications from Stanford’s <a rel="noreferrer noopener" href="https://bmir.stanford.edu" target="_blank">Center for BioMedical informatics Research</a> (BMIR) will be center stage. BioPortal and CEDAR Technical Program Manager John Graybeal has been selected to lead the 5-day workshops for the <a href="https://deic.dk/en" target="_blank" rel="noreferrer noopener">Danish e-Infrastructure Cooperation</a> (DeiC), established to support Denmark as an e-Science nation through delivery of e-infrastructures (computing, storage and network) to research and research-based teaching. The GO FAIR M4M team needed highly performant systems to meet the 5 goals of the M4M workshops: <ul class="wp-block-list"><li>Assess the state of metadata practices in the various scientific communities, look for improvements of the current fragmentation and promote good FAIR compliant practices.</li><li>Using the FAIR principles as a guide, define essential metadata elements and standards to support F, A, I, and R by machines, drawing on the deep domain knowledge of existing communities.</li><li>Formulate these decisions as machine-actionable templates in a unified way;</li><li>Register these templates such that they are Openly accessible and available for re-use by tools that can render these templates in familiar, easy to use web forms, APIs, or other capture tools.</li><li>Bundle appropriate M4M metadata categories and register them as FAIR compliant metadata components, ensuring higher degrees of F, A, I, and R by machines.</li></ul> <a rel="noreferrer noopener" href="https://metadatacenter.org" target="_blank">CEDAR</a> and BioPortal uniquely provide a working solution that combines principled and open metadata definitions in machine-actionable templates, and full support for semantic principles and standards, including any ontology term registered in the community-based BioPortal ontology repository. With 15 years of semantic repository services, and 4 years of end-to-end metadata services, the BioPortal and CEDAR services provide an ideal platform for demonstrating FAIR capabilities that support the straightforward production of standardized metadata. And because BioPortal lets users register any ontology—visible only to CEDAR if desired—users need not worry that their terms will not be available for annotation with CEDAR. The first CEDAR demonstrations for this training are captured in short training videos in the <a rel="noreferrer noopener" href="https://www.youtube.com/playlist?list=PLRFrKQ_tBSlssjQDK0333JGNeJncyhOcj" target="_blank">M4M DeiC YouTube playlist</a>, including demonstrations of CEDAR sharing, OpenView, composition, and semantic features leveraging the BioPortal ontology repository. Check them out! <div class="wp-block-image"><figure class="aligncenter size-large is-resized"><img fetchpriority="high" decoding="async" src="https://www.bioontology.org/wp-content/uploads/2020/07/YouTube-M4M-DeiC-Playlist-Screen-Shot-20200731.png" alt="" class="wp-image-798" width="252" height="340" srcset="https://www.bioontology.org/wp-content/uploads/2020/07/YouTube-M4M-DeiC-Playlist-Screen-Shot-20200731.png 453w, https://www.bioontology.org/wp-content/uploads/2020/07/YouTube-M4M-DeiC-Playlist-Screen-Shot-20200731-223x300.png 223w" sizes="(max-width: 252px) 100vw, 252px" /></figure></div> ]]></content:encoded> </item> <item> <title>Missing a term? BioPortal speaks OntoloBridge</title> <link>https://www.bioontology.org/missing-a-term-bioportal-speaks-ontolobridge/</link> <dc:creator><![CDATA[John Graybeal]]></dc:creator> <pubDate>Sat, 01 Aug 2020 03:37:10 +0000</pubDate> <category><![CDATA[Happenings]]></category> <category><![CDATA[News]]></category> <category><![CDATA[OntoloBridge]]></category> <category><![CDATA[OntoPortal Virtual Appliance]]></category> <category><![CDATA[Term requests]]></category> <guid isPermaLink="false">https://www.bioontology.org/?p=788</guid> <description><![CDATA[Registered BioPortal users viewing ontology terms in BioPortal can use the New Terms Request tab to fill out an OntoloBridge request form for their needed term.]]></description> <content:encoded><![CDATA[ For several years, BioPortal team has contributed to a new semantic service for requesting ontology terms. The product is called <a href="https://physician-news.umiamihealth.org/novel-platform-connects-users-and-developers-of-scientific-vocabularies/">OntoloBridge</a>, and it lets users request terms (and eventually, changes to terms) for any ontology. Developed by the University of Miami’s <a href="https://ccs.miami.edu/focus-area/drug-discovery" target="_blank" rel="noreferrer noopener">Institute for Data Science and Computing</a>, Stanford University’s <a rel="noreferrer noopener" href="https://bmir.stanford.edu" target="_blank">Center for Biomedical Informatics Research</a>, and <a rel="noreferrer noopener" href="https://collaborativedrug.com" target="_blank">Collaborative Drug Discovery, Inc.</a>, OntoloBridge lets users or other systems make a request for an ontology term in a particular ontology. Often users looking at an ontology have no idea how to request a new ontology term, or whom to ask; and if they are using a tool that is itself using an ontology, the end user may not even know what ontology is being used. OntoloBridge solves this problem by providing an API for requesting ontology terms, and curating the requests that are received. BioPortal has implemented an interface to this API, so that if an ontology manager wants people to be able to easily request new terms for their BioPortal-displayed ontology, they simply ask the <a href="mailto:support@bioontology.org">Stanford BioPortal</a> or <a href="mailto:info@ontolobridge.org">University of Miami OntoloBridge</a> team to enable the request system for their ontology. <div class="wp-block-image"><figure class="aligncenter size-large is-resized"><img decoding="async" src="https://www.bioontology.org/wp-content/uploads/2020/07/BioPortal-OntoloBridge-Screen-Shot-20200731-1024x620.png" alt="" class="wp-image-790" width="668" height="404"/><figcaption>After selecting the ‘cell’ concept in the Protein Ontology, a logged-in user clicks on New Term Requests to see and fill out the OntoloBridge request form.</figcaption></figure></div> When the BioPortal ontology has OntoloBridge requests enabled, the registered BioPortal user viewing ontology terms in the ontology’s class tree can use the New Terms Request tab to fill out a request form for the term he or she needs. BioPortal will forward this request to OntoloBridge, whose operations team will pass the request on to the appropriate ontology manager or ontology request system. The OntoloBridge term request service can also be enabled in any OntoPortal Virtual Appliance, after consultation with the University of Miami team. In the coming year, BioPortal plans to implement a configurable instructions field for each OntoloBridge-enabled ontology, and make it possible to see the status of term requests previous made for that ontology. ]]></content:encoded> </item> <item> <title>Non-breaking news! Changes coming to BioPortal</title> <link>https://www.bioontology.org/non-breaking-news-changes-coming-to-bioportal/</link> <dc:creator><![CDATA[John Graybeal]]></dc:creator> <pubDate>Fri, 10 Apr 2020 09:18:00 +0000</pubDate> <category><![CDATA[Happenings]]></category> <category><![CDATA[News]]></category> <category><![CDATA[AllegroGraph]]></category> <category><![CDATA[Backend Triple Store]]></category> <category><![CDATA[Maintenance Period]]></category> <category><![CDATA[OntoPortal Alliance]]></category> <category><![CDATA[OntoPortal Virtual Appliance]]></category> <guid isPermaLink="false">https://www.bioontology.org/?p=751</guid> <description><![CDATA[We'll have a BioPortal maintenance period this Saturday evening, to prepare for bigger announcements in coming weeks.]]></description> <content:encoded><![CDATA[ <div class="wp-block-image"><figure class="alignright size-large is-resized"><img loading="lazy" decoding="async" src="https://www.bioontology.org/wp-content/uploads/2020/04/image.png" alt="Construction ahead" class="wp-image-756" width="66" height="66"/></figure></div> We have a lot to share, but today we have to focus. We want to get the word out about an upcoming maintenance period (this weekend!), but there are so many reasons for it… Well, let’s get the notification out first. This weekend and next week we plan to make some minor modifications under the BioPortal hood. If things go well, you won’t even know anything has changed. We’ll start after 9 PM (GMT-7) Saturday, and the only thing you might notice is a job or UI going down for a minute or two. Or not even that. Once that’s taken care of, a few changes to the UI will follow, likely Tuesday morning. (You won’t see most of those either, they’re on the Admin pages.) So why do this—and use up your valuable reading time? We’ve been working on several significant projects for quite a while, as part of our overall strategic plan. The first release for some of these changes will be most visible in our OntoPortal Virtual Appliance, long overdue for a new release [1]. But to keep BioPortal and OntoPortal code aligned (more on that later)[2], we’re also updating the production system—what you see and use. In a worst case scenario this weekend, we might need a few hours of down time on Sunday to identify and address issues. (Just wanted to let you know what was up in case that happened.) But in coming days, weeks, and months, you’ll see more announcements on social media for BioPortal, and our partner organizations. [3] Thanks for your patience! We look forward to the enhancements coming your way. <figure class="wp-block-image size-medium is-resized wp-block-gallery columns-3 is-cropped"><img loading="lazy" decoding="async" src="https://www.bioontology.org/wp-content/uploads/2020/04/Prototype-OntoPortal-Appliance-Logo-300x113.png" alt="" class="wp-image-760" width="388" height="147"/><figcaption>Hints are everywhere</figcaption></figure> <div class="wp-block-image"><figure class="alignleft size-thumbnail"><img loading="lazy" decoding="async" width="150" height="150" src="https://www.bioontology.org/wp-content/uploads/2020/04/OntoPortal-Alliance-Logo-with-Text-150x150.png" alt="OntoPortal Alliance Logo" class="wp-image-761"/></figure></div> <div class="wp-block-image"><figure class="alignright size-large is-resized"><img loading="lazy" decoding="async" src="https://www.bioontology.org/wp-content/uploads/2020/04/Allegrograph-Logo.png" alt="AllegroGraph Logo" class="wp-image-763" width="320" height="80"/></figure></div> References [1] That’s a hint. <a href="https://www.bioontology.org/mediawiki/index.php?title=Category:NCBO_Virtual_Appliance">The release</a> really is coming soon. [2] Another hint: There are technical implications of [3]. More soon! [3] Have you heard about the <a href="https://ontoportal.org">OntoPortal Alliance</a> yet? ]]></content:encoded> </item> </channel> </rss>