NCI EVS changes EVS server content for production
Announced June 15, 2012
The following vocabularies have been released to the Production servers of LexEVS 5.1 and 6.0:
- NCI Thesaurus 12.05d (end-May 2012)
- Gene Ontology (GO) June2012
- HGNC June2012
- NDF-RT June2012
This mapping has also been updated on LexEVS 6.0 (it is not supported on 5.1):
- NCIt to HGNC Mapping (6.0 only)
This affects these EVS servers and browsers, as well as other downstream applications:
- NCI LexEVS 6.0 API
- NCI Term Browser
- NCI Thesaurus Browser
- NCI Metathesaurus Browser
- NCI LexEVS 5.1 API
- NCI 5.1 Terms Browser
cTAKES 2.5 released
Announced May 4, 2012
There are good number of upgrades and changes for this release, like a new Assertion annotator, a newer Part Of Speech (POS) model trained on more clinical data, an additional Sectionizer, updates to the Co-ref Resolver, a Semantic Role Labeler (SRL) as part of the dependency parser, and updates to OpenNLP 1.5.
LexEVS 6.0.3 and 6.0.4 now available
Announced May 2, 2012
The next fix releases of LexEVS are now available. 6.0.3 has been tested by QA at NCI and 6.0.4 by the development team. Both can be used as a stand-alone install and as a fix pack on top of any 6.0.x install. Both include all previous fixes. Follow the links to find the readme files to see what's included.
NCI LexEVS 5.0 retired
Announced May 2, 2012
Retirement of NCI's LexEVS 5.0 terminology server instance is now scheduled for May 3, 2012. LexEVS 5.0 has been deprecated since late 2010, and previous announcements have encouraged users to migrate to the newer LexEVS 5.1 or 6.0 servers before the original May 1 retirement date.
If you still use the 5.0 server, please contact us at NCIThesaurus@mail.nih.gov so that we are aware of your needs and can help you migrate. Information about migrating can also be found for 5.0 and 6.0.
AMIA working group hosts terminology presentations
Announced April 17, 2012
AMIA's Knowledge Representation and Semantics Working Group has been hosting webinars in the past month. At AMIA's working group website you will find the videos from domain experts on LOINC, RxNorm, SNOMED CT, and ICD-10.
cTAKES 2.0 released
Announced April 9, 2012
cTAKES 2.0 was released recently. There have been major changes to the common type system and therefore not much other function has been included. In this release cTAKES merges the icTAKES and cTAKES. There is only one download for using cTAKES.
CTS2 BioPortal connection
Announced April 3, 2012
The second of two videos has been posted about CTS2. This time Kevin Peterson talks about a specific use case, CTS2 Over BioPortal. A wrapper has been started which shows off the benefits of CTS2 for a terminology server - in particular RDF triples. This is, of course, not the only benefit, but it is the focus of this presentation.
NCI EVS LexEVS server 5.0 to be removed
Announced March 28, 2012
NCI plans to retire the LexEVS 5.0 terminology server on May 1, 2012. It has been deprecated since late 2010, and previous announcements have encouraged users to migrate to the newer LexEVS 5.1 or 6.0 servers. If you still use the 5.0 server, please contact us at NCIThesaurus@mail.nih.gov so that we are aware of your needs and can help you migrate. Information about migrating can be found in the migrations guides for both LexEVS 5.1 and 6.0.
VKC is showing off CTS2
Announced March 27, 2012
A new video has been introduced showing off the various functions specified in CTS2. We called it CTS2 In Action since it is more than just an overview. Watch as Kevin Peterson walks you through several examples, such as, searching for concepts, a mappings viewer, change sets, and concept mapping.
LexEVS 6.0.2 Available
Announced March 2, 2012
LexEVS 6.0.2 was released with key fixes. LUI lengths have changed for RRF loads, OWL export was changed for CUI and TUI properties, DB collation can be configured in the properties file, and more. See the latest LexEVS fixes for installation instructions and more information.
Semantator's initial release now available
Announced February 23, 2012
The ontology CNTRO.OWL is used to allow temporal information of clinical data to be semantically annotated and queried and to use inference to expose new temporal features and relations based on the semantic assertions and definitions of the temporal aspects in the ontology. Using this ontology Semantator 1.0, a Protege plug-in, can take clinical documents and allow real time annotation. The first release of this annotator can use other annotators in the back-end to semi-automatically flag annotations.
VKC launches its third cloud computing image
Announced February 6, 2012
The VKC is proud to announce our third cloud computing resource. This Amazon Web Service (AWS) machine image (AMI) is for use of the LexEVS Distributed environment embedded into a Linux distribution. This image is graced with a small set of standard terminologies making it even easier for you to utilize these services. An AWS account is required to use these services, but this is a very inexpensive way and very efficient way to use these EVS resources. Start with the VKC Cloud Computing Services overview to get started with our new LexEVS Distributed image. We plan to make some refinements to the images we have thus far. Let us know what you think.
VKC Wiki has moved to Confluence
Announced January 31, 2012
All remaining pages are being redirected to this wiki as of January 31, 2012. You will find the same great content on the wiki here. If you see any issues with page content please let us know. We promote this site as a community effort. While the VKC remains the proprietor of the site the community is welcome to participate. You can obtain edit rights to VKC pages by specifying your involvement with VKC or LexEVS when you create a new account or just let us know you would like to be involved.
NCI CBIIT announces caBIG® Community Code Resource Directory
Announced January 31, 2012
The NCI Center for Biomedical Informatics and Information Technology (CBIIT) is pleased to announce the launch of the caBIG® Community Code Resource Directory, a resource intended to promote the exchange of community-developed digital capabilities supporting cancer research. This dynamic directory provides pointers to resources that have been developed in support of local informatics needs which may also be of value to the broader cancer research community.
The launch of the Community Code Resource Directory represents a strengthening of NCI’s commitment to a collaborative development ecosystem. This directory will grow quickly to include capabilities across many biomedical domains of importance to the research community, and we encourage you to check back frequently as new resources are added. We also encourage you to suggest code to be added to this resource – you can do so by e-mailing email@example.com.
NCI EVS changes EVS server content for testing
- NCIt 12.02d
- ChEBI March 2012
- GO March 2012
- HGNC (HUGO) March 2012
- MA (Mouse Anatomy) March 2012
- NDFRT March 2012
NCI EVS changes EVS server content for production
Announced March 23, 2012
The following vocabularies have been released to the Production servers of LexEVS 6.0:
- Gene Ontology February 2012
- HUGO February 2012
- OBI San Diego
- NCI Thesaurus 12.01f
This affects these EVS servers and browsers, as well as other downstream applications:
Next Protege 3 patch released
Announced January 13, 2012
A number of fixes and updates to Jena included in Protege 3.4.8.
NCI EVS changes EVS server content for testing
Announced January 13, 2012
The following vocabularies have been released to the staging server of LexEVS for testing by downstream applications. These have all been released under versions 5.0, 5.1, 6.0 of the LexEVS server:
- Gene Ontology December 2011
- HUGO December 2011
- NDF-RT December 2011
- NCI Thesaurus 11.11d
- NCI Metathesaurus 201109
cTAKES road map published
Announced January 5, 2012
The VKC, in conjunction with the OHNLP consortium, has published a cTAKES road map. All previous releases are listed as well as a look into the future.
cTAKES 1.3 released
Announced December 23, 2011
Inclusion of complete UMLS dictionaries tops off the functions for the cTAKES 1.3 release. You must provide a UMLS license but you no longer must download and install separately the dictionaries. They are ready out-of-the-box. Also two new annotators are included: Coreference resolver and Constituency Parser.
VKC launches its second cloud computing image
Announced December 14, 2011
The VKC is proud to announce our second cloud computing resource. This is another Amazon Web Service (AWS) machine image (AMI). This image is for use of the LexEVS Distributed environment and is embedded into a Linux distribution. An AWS account is required to use these services, but this is a very inexpensive way to use these EVS resources without having to go through the install process. Start with the VKC Cloud Computing Services overview to get started with our new LexEVS Distributed image. Our next image will be the same except with some standard terminology content already loaded.
- LexEVS 6.0.1 released
Announced November, 14, 2011
The next set of fixes is now available for download. Please see the LexEVS pages for more information.
- NCI releases 2.0 version of NCI Term Browser and NCI Metathesaurus Browser
Announced November 9, 2011
These browsers offer important new data and functionality, based on the LexEVS 6.0 Terminology Server. The new server and browsers provide additional support for value sets, mappings between terminologies, local extensions to a terminology, and content creation and editing, aligned with the HL7 draft standard for trial use (DSTU) Common Terminology Services 2 (CTS 2) specification.
- NCI EVS changes EVS server content for testing 5.0 , 5.1 , 6.0
Announced November, 29, 2011
The following vocabularies have been released to the staging server of LexEVS for testing by downstream applications. These have all been released under versions 5.0, 5.1, and 6.0 of the LexEVS server:
Gene Ontology November 2011, HUGO November 2011, NDF-RT November 2011, NCI Thesaurus 11.10e, Zebrafish October 5 2011.
Also available on LexEVS 6.0 only: HL7 V3 R2.36.
- Vocabulary and Common Data Elements Workspace Virtual Journal Club Started
Announced October 25, 2011
The Vocabularies and Common Data Elements Workspace (VCDE WS) has started up a Virtual Journal Club. The VCDE WS Virtual Journal Club is meant to build upon the familiar journal club activity found in most collegiate and graduate schools. Further, it will borrow from the familiar "seminar series", also prevalent at most institutions of higher learning. Finally, we are including a more recent element of knowledge sharing, that encompassing web sites, blogs, and social media streams, etc., that can be part of the Journal Club presentations and knowledge sharing.
- cTAKES 1.2 released
Announced October 24, 2011
Significant changes toward installability have been released in the new cTAKES 1.2. A new (beta) annotator called SideEffect is also introduced. This annotator extracts physician-asserted drug side effects from clinical notes.
- Vocabulary Views Newsletter Volume 3 Issue 1 now available
Announced October 21, 2011
The Vocabulary Knowledge Center invites you to read the latest issue of Vocabulary Views , a newsletter that describes recent activities at the Vocabulary Knowledge Center. This issue includes VKC presentations at the AMIA 2011 Annual Symposium, updates on the Common Terminology Services 2 (CTS2) specification, LexEVS cloud computing, Semantic Web Technologies, and more.
- VKC launches its first cloud computing image
Announced September 16, 2011
The VKC is proud to announce that we have just published our first cloud computing resource. This is an Amazon Web Service (AWS) machine image (AMI). This first image can be used to understand the value and the programming of the LexEVS terminology server. An AWS account is required to use these services, but this is a very inexpensive way to try out a tool without having to go through the install process. Start with the VKC Cloud Computing Services overview to get started.
- cTAKES overview video posted
Announced September 6, 2011
cTAKES has been available for some time now. This has typically been a developers tool. As cTAKES starts to transition to an end user tool as well as a developers tool, a simple explanation of the tool was developed. Check the OHNLP documentation to view the video.
- New article - Why Ontologies in Healthcare?
Announced August 31, 2011
An article was recently published that is an answer to the question, "what can OWL do?" Our Terminology 101 page now links to this article which answers the question, Why Do We Need Ontologies in Healthcare Applications?
- New LexEVS Guide for Eclipse SpringSource Tools published
Announced August 23, 2011
The spring framework has emerged over the last few years as a versatile and efficient support structure for multiple types of Java applications. The MVC component facilitates the development of rich web-driven applications. The SpringSource tool suite(STS) is an Eclipse derivative software package that bundles the necessary tools to develop efficiently with the Spring framework. The Spring 3 MVC project is a Maven compliant project and this guide will make use of it to include a LexEVS dependency.
- Difference between NCIThesaurus and NCIMetathesaurus published
Announced August 16, 2011
Have you ever considered the difference between the NCI Thesaurus and NCI Metathesaurus? On the surface it appears that the NCI Thesaurus is simply a subset of the NCI Metathesaurus, but then why have both? A new page has just been published showing the key differences between these two vocabularies.
- Semantic Media Wiki 1.6 Released
Announced August 5, 2011
The newest version of Semantic MediaWiki is now out. It now supports SPARQL 1.1 RDF stores. Specifically support for using SPARQL-compatible RDF stores for managing data (including query answering). This is possible by exploiting the new SPARQL 1.1 Update capabilities for writing, and SPARQL Query for accessing semantic data. See the SMW site for more information and other functions added to this release.
- Code-a-thon Project Enhances Veterans' Electronic Medical Records
Announced July 29, 2011
Representatives from caBIG® "NCI Team Blue" took the second place prize at the Health 2.0 Developer Challenge Code-a-thon in Washington, DC on June 11. Their work demonstrates how caBIG® capabilities could be deployed to create information value for Veterans, and show how caBIG® can create value for users with the investment of just one day of coding time. Watch a video about NCI Blue, a Hack-A-Thon Project and read our description of this demonstration.
- Protege 4.1 released
Announced July 27, 2011
Stanford has moved Protege 4.1 from a beta to a supported release.
- NCI Thesaurus changes require feedback
Announced July 13, 2011
Several outdated properties will be deprecated and deleted from the NCI Thesaurus. The NCI EVS team would like to get feedback on these changes if possible before they are implemented by July 21, 2011. Click this changes link to see the proposed changes. If applications need time to make fixes then the deprecation timeline could be adjusted.
- Exciting news about CTS 2
Announced June 26, 2011
The CTS 2 submission team is pleased to let you know that the Mayo Clinic CTS 2 Submission was approved by the OMG Analysis and Design Task Force, Architecture Board and Tech Committee this past week. The submission will now become an OMG beta specification and will be available for implementers. A finalization task force was formed with Mayo Clinic as chair and, over the next year, they will be accepting technical correction feedback. There is much excitement in the community for CTS 2. Continued publicizing and education for CTS 2 will be presented at the OMG SOA in Healthcare Conference in July and a "CTS 2" day is planned at the September OMG meeting.
- NCBO Releases BioPortal 3.0
Announced May 19, 2011
The National Center for Biomedical Ontology (NCBO) released BioPortal 3.0 today. Refer to the BioPortal Releases for details.
- New Semantic Web Technologies section on the VKC
Announced May 11, 2011
The power and future of a connected Internet comes in the form of the Semantic Web. Machine readable information connects the web in ways not possible before. That's right. It's all semantics. Read here our take on the tools, trends, and technologies.
- HHS Health 2.0 Developer Challenge
Announced June 9, 2011
HHS is sponsoring their Code-a-thon again this Saturday. This event brings together developers, designers, and raw data sets to build new applications and tools for improved health care. Our team project, presented by Larry Brem and Mark Adams, will be to leverage the CBIIT infrastructure, such as the EVS (Enterprise Vocabulary Services), to construct automated "roll-over" definitions of medical terminology in a patient's electronic medical record, as produced by the Veteran Administration's Blue Button initiative.
- Life Sciences Domain Analysis Model 2.2 released
Announced May 4, 2011
The LS DAM is a foundational component for achieving semantic interoperability among the various applications across caBIG® and is bound to the ISO 21090 data type standard. A survey was taken on multiple public 'omics databases allowing a gap analysis top be performed. See the difference on the LS DAM page along with other major changes in this release.
- LexEVS Roadmap created
Announced April 22, 2011
A simple roadmap of the past and future releases of LexEVS has replaced the main LexEVS page. All the same content is still available. The LexEVS main page now uses the roadmap for navigation to LexEVS releases.
- NCI Term Browser demonstration video
Announced April 15, 2011
The NCI Term Browser version 1.2 has been discussed a couple of times on teleconferences in the last 3 months. Here's your chance to learn how the browser works in under 10 minutes. Check out the video (11 MB, 8.5 Minutes) just uploaded to the VKC to get a quick overview of the browser's user interface like searching, content, and navigation.
- CDE Browser 4.0.2 released
Announced Mar 31, 2011
The latest version of the CDE Browser has just been deployed. Check out the release notes for new features and bug fixes.
- LexWiki Publisher 2.0 is released
Announced Mar 15, 2011
Semantic MediWiki (SMW), LexWiki, LexEVS, and your ontology: It all comes together in this second release of LexWiki Publisher. Configurable for any terminology that can be loaded into LexEVS, now you can use LexWiki Publisher to publish your terminology into a SMW instance with a simple configuration file.
- LexEVS Migration from version 5 to 6
Announced Mar 4, 2011
As more people move to the recently announced LexEVS 6.0, we are glad to announce that code migration documentation is available. A migration tips page has just been added with a section for string searches that point you to places in your code where attention needs to be given. The sections after that describe what kind of changes will need to be made in that area.
- New LexEVS OWL export guide
Announced Mar 1, 2011
Need your terminology in OWL. After being loaded into LexEVS 6.0 you can export any terminology in OWL RDF format. The VKC recently published a guide to help you through the process.
- ISO 21090 is "Published"
Announced Feb 09, 2011
ISO moved the 21090 standard for health informatics to "Published" on Feb 9, 2011. This standard provides a set of datatype definitions for representing and exchanging basic concepts that are commonly encountered in healthcare environments.
- NCI Browsers Installation Instructions
Announced Feb 09, 2011
The VKC just added new NCI Browsers Installation Instructions to our site. Did you know that you can download and install this browser? It will work over your local copy of NCI terminologies such as NCI Thesaurus or your own terminology loaded into LexEVS.
- Pre-packaged CDE downloads
Announced Feb 03, 2011
A new caDSR CDE Downloads page for commonly requested or required downloads of CDE content has been created. The page is updated on a monthly basis and may help you find reusable CDE content.
- LexEVS 6.0 officially released
Announced Feb 01, 2011
The VKC is happy to announce that the latest version of LexEVS was officially released today. It has critical functionality based on the future of caBIG's semantic infrastructure such as an implementation of HL7's draft CTS 2 specification; mapping associations between terminologies; value set, pick list, and versioning support; authoring API and loader enhancements; and a new OWL/RDF exporter. Other NCI tools will start to take advantage of this release right away. Take a look and you can reap the benefits as well. Older LexEVS releases move toward retirement. 5.1 is depricated but supported through 2011. 5.0 is moving to retirement but servers will stay up for this year. 4.2 is now retired and will be unavailable after the last migrations. All previous releases have been retired.
- VKC Forum use tip
Announced Jan 26, 2011
It has come to the attention of the VKC that some users may not get notified via email of forum thread updates that they would be interested in. For example you may not get notified when someone replies to a new topic that you created. This only affects users who created an account before Jan 2011. Check out the work around.
- Parts of SNOMED CT® are free
Announced Jan 28, 2011
IHTSDO® "announced a new policy to enable free use of English-language SNOMED CT terms and identifiers" today. There are restrictions that apply. Take a look at their press release for more information.
- The VKC announces LexWiki 2.0
Announced Jan 3, 2011
The Vocabulary Knowledge Center is pleased to announce the second major release of LexWiki. This release brings all the MediaWiki extensions up to their latest versions, simplifies the installation, and enhances the ability to make concept proposals. The basic premise of LexWiki remains the same as a collaborative terminology authoring platform. See the LexWiki page for more information.
- cTAKES 1.1 announced
Announced Dec 22, 2010
The SHARP 4 NLP team is excited to announce the release of cTAKES 1.1. This is the first cTAKES release based on efforts completed through the ONC-funded SHARP project. Information and downloads are also available on the OHNLP News page.
- caDSR CDE canned downloads
Announced Dec 17, 2010
The CDE Browser can be used to download collections of CDEs in Excel or XML Format. However, it is not always easy to find the desired collection, as CDEs are organized in the Navigation Tree by Context, not topic. Attempting to download all the Released CDEs would result in a file that is too large for an Excel download. Check the CDE canned downloads page for fairly stable collections of CDEs. You can even propose your own collection that you would like to see.
- WikEd Demo Video
Announced Nov 29, 2010
Along with the Choosing another Wiki editor page, we have created a demo video for the WikEd MediaWiki editor.
Note: This content was removed after migration to Confluence.
- LexEVS 6.0 Documentation is being written
Announced Nov 17, 2010
As we draw closer to December and the reference implementation for CTS 2, the documentation for LexEVS 6.0 is being written. Parts that come over from the previous version are being reworked as well.
- Choosing another Wiki editor
Announced Nov 15, 2010
Do you edit any of the caBIG® knowledge center (or other Media Wiki pages) but don't have the rich text editor extension? If you are looking for a little better editor than the basic editor that comes with Media Wiki then look at our new page describing how and why you might choose WikEd.
Note: This content was removed after migration to Confluence.
- caDSR Form Builder 4.0.3
Announced Oct 22, 2010
This release of Form Builder is designed to better support the retrieval of collections of caDSR forms metadata to reuse in customizing clinical data management systems. Among the new features are a "Forms Cart" which is used to create the collection, a collapsible Permissible Values List for improved viewing/editing, and implementation of an 'IsEditable' flag. To learn more, please visit the caDSR Form Builder Tool 4.0.3 Release Notes page.
- New LexEVS Widget Library
Announced Oct 14, 2010
The widget code is not necessarily new, but a new widget library page has been put together for LexEVS developers to utilize. Take a look and perhaps get some useful code for your application.
- ICD-10 on NCI Term Browser
Announced Sept 16, 2010
ICD-10 has been published as a search-able vocabulary in the NCI Terminology Browser. An ICD-10 page has been added to the Index of Terminologies on the VKC. NCI is working on a version of ICD-10-CM that it is hoped will be available in the browser in the next few months.
- LexEVS 6.0 highlights published
Announced Sept 9, 2010
The Vocabulary Knowledge Center has just published a consolidated look at the upcoming LexEVS 6.0 release. Due to be out in December, this release makes great strides as a reference implementation for CTS 2.
- Vocabulary Views Newsletter Volume 2 Issue 2 now available
Announced Sept 2, 2010
The Vocabulary Knowledge Center invites you to read the latest issue of Vocabulary Views , a newsletter that describes recent activities at the NCI caBIG® Vocabulary Knowledge Center. This issue includes: Information regarding the upcoming annual meeting, updates on LexEVS 6.0 development, Common Terminology Services 2, LexRDF, and the new LexWiki Publisher.
- NCI Thesaurus and NCI Metathesaurus history published
Announced August 27, 2010
Ever wanted to see what's been going on with these terminologies? Would you like to check for recent changes. We have published the changes since 2004 for these popular terminologies. These are linked in from the Index of Terminologies for the NCI Thesaurus and NCI Metathesaurus.
- Semantic Infrastructure 2.0 Roadmap out for review
Announced August 26, 2010
Right on the heels of the caGrid 2.0 Roadmap is your chance to help shape the future of caBIG® with the next version of the Semantic Infrastructure. Charlie Mead and Dave Hau have asked the community to share their thoughts from now up to the caBIG® Annual Meeting. They will publish the iterative development of this document every two weeks until the annual meeting. Directions for providing your input are on the roadmap page.
- caGrid 2.0 Roadmap out for review
Announced August 8, 2010
Don't miss this great opportunity to help shape the future of caBIG®. Charlie Mead and Avinash Shanbhag have asked the community to share their thoughts from now up to the caBIG Annual Meeting. They will publish the iterative development of this document every two weeks until the annual meeting. Directions for providing your input are on the roadmap page.
- Request For caDSR and EVS End User Stories
Announced August 5, 2010
We are interested in hearing about uses of the caDSR or EVS open source software, caDSR data elements, Forms or UML Models, or EVS terminology. We have collected many stories from our C3D (Cancer Central Clinical Database) adopters and users, about how they use the caDSR to hold the variables to describe their clinical trials and research. Now we're interested in expanding this inventory with examples from other users of the data standards registry/repository and terminiologies.
Please send replies to Denise Warzel with the following information: Institution name, Project name, PI name, Purpose: (Brief statement about how you are using the infrastructure), Status: (Experimenting/Exploring, Current Production Work, Completed Study, building interoperable system, etc), Approximate end date of the project.
- New education for Curation Tool 4.0.2
Announced August 02, 2010
The 4.0.2 release of the Curation Tool, announced previously, has a new course to go with it, Intro to CDE Curation Tool 4.0.2. The purpose of the course is to provide new and existing users with an overview of the primary tool functions, the new user interface layout, menu items, basic search functionality and the new action icon (Lesson 6). The course will be available for download in the caBIG® Learning Management System.
- The WHO-IHTSDO memorandum of agreement is official
Announced July 21, 2010
The International Health Terminology Standards Development Organization (IHTSDO) and The World Health Organization (WHO) have signed a collaborative agreement, enabling harmonization - as complementary tools - of WHO Classifications and SNOMED CT, for the benefit of citizens around the world.
- NCBO BioPortal 2.5 Release
Announced July 15, 2010
The National Center for Biomedical Ontology is pleased to announce the release of NCBO BioPortal 2.5, a Web-based platform for browsing, visualizing, mapping, and commenting on biomedical ontologies and terminologies. The new release of NCBO BioPortal includes many new features, Web services, and bug fixes.
- LexWiki Publisher 1.0 Release
Announced July 9, 2010
Now those who install the LexWiki can do more than play with a demonstration version of a cool tool with the release of the LexWiki publisher. The publisher allows users to pull information from their LexEVS installation and publish it to the LexWiki in a few steps. For this first release the ontologies allowed to be published are limited to NPO, BGT, CTCAE, and Radlex. Future releases will look to reduce that restriction.
- Metathesaurus Browser 1.2 Release
Announced July 7, 2010
The EVS team is pleased to announce the NCI Metathesaurus (NCIm) 1.2 Release. The NCIm Browser gives user-friendly access to 76 biomedical terminologies cross-mapped to capture shared meanings. Key features of this new release include improved navigation and enhanced search.
- Terminology 101 paper just published
Announced July 2, 2010
One of our esteemed experts at the Vocabulary Knowledge Center has just published a paper for the beginner in the world of ontologies. This paper goes through the What, Why, How, and Where of terminologies. It explains, in simple terms, what you need to know to get started. Don't miss the other content on our beginner page as well.
- The WHO-IHTSDO memorandum of agreement is official starting at July 2010.
Announced July 1, 2010
A Collaborative Arrangement between the International Health Terminology Standards Development Organisation (IHTSDO) and The World Health Organization (WHO) has been officially signed since July 2010.
The Collaborative Arrangement enables harmonization - as complementary tools - of WHO Classifications and SNOMED CT for the benefit of citizens around the world. When used together appropriately, they make it easier to summarize information from individual patients' health records into aggregated results needed for health policy, health services management, and research. WHO and IHTSDO aim to increase collaboration in order to create and maintain jointly usable and integrated classification and terminology systems to make efficient and effective use of public resources and avoid duplication of effort. This is essential to create health information's standards as a common language worldwide.
WHO Classifications are used to capture key information on diseases, disability, interventions and other indicators of population's health. Main classifications such as the ICD (International Classification of Diseases), in use for more than 100 years worldwide, provide data on life expectancy, causes of death, and inform the plans and decisions of health authorities in many countries.
SNOMED CT is a standardized health terminology that represents clinical concepts in a consistent, and comprehensive way in health records. Managed by the IHTSDO, it is used for this purpose and others in countries around the world. Given the emergence of Electronic Health Records (EHRs), the use of standardized terminologies has become more important for meaningful exchange of data in health information systems.
This collaboration arrangement will be used to build maps and linkages between ICD and SNOMED CT for automated processing of data to improve coding and information exchange. It will also enhance the work on the revision of the ICD for its 11th revision.
This new arrangement supports the aims of WHO and IHTSDO to enhance health through better health information. Synergies between WHO classifications and SNOMED CT have the potential, through better information, to improve the accuracy, the reliability, and the quality of health and health care; to eliminate gaps in information; and to control costs.
- NCI Terminology Browser
Announced June 25, 2010
The NCI BioPortal Browser has been officially retired. The flagship browser for EVS is now the NCI Terminology Browser, located at NCI Terminology Browser. The NCI Terminology Browser has a cleaner interface, improved content and features, and improved performance.
- Arch-VCDE WS face to face meeting presentations posted
Announced June 08, 2010
Not only have they been posted but the agenda has been modified as well to contain links for each presentation at the recent face to face meeting. This will help you to easily locate the materials for any of the great sessions.
- Vocabulary Views Newsletter Volume 2 Issue 1 now available
Announced June 02, 2010
The Vocabulary Knowledge Center invites you to read the latest issue of Vocabulary Views , a newsletter that describes recent activities at the NCI caBIG® Vocabulary Knowledge Center. This issue of Vocabulary Views includes:
HL7 Common Terminology Services (CTS) 2.0; LexEVS 6.0 and CTS 2; Availability of ECCF Training Materials; openMDR and CSHARE Integration; Release of LexEVS 5.1.4; Upgrade of the LexEVS iPhone Application; Announcement of the Community Code; Contribution Process
- caDSR browser support
Announced May 18, 2010
Please note that caDSR will be phasing out support for Microsoft Internet Explorer 6.0. We will continue to support Internet Explorer 7.0 and above, and Firefox 3.0 and above, but testing will cease on IE 6.0.
- Improving Search Capabilities Across caBIG®
Announced May 07, 2010
In our continuing effort to streamline content and facilitate searching across caBIG® resources, we have deployed a dedicated Google Search appliance.
Search results from the caBIG® Community website and Knowledge Center wiki environment now yield a comprehensive list of resources related to your search term.
- Abstracts Are Now Being Accepted for Posters and Exhibits at the 2010 caBIG® Annual Meeting
Announced May 06, 2010
Poster abstracts and exhibitor applications are now being accepted for the 2010 caBIG® Annual Meeting, to be held September 13-15 in Washington, D.C.
Accepted applications will be included in the 2010 caBIG® World's Fair Expo, an annual event that features posters, exhibits, and demonstrations of caBIG® tools.
- caGrid Portal 3.0 has been Released and is Immediately Available
Announced May 04, 2010
The Portal team is pleased to announce the release of caGrid Portal version 3.0. This release is an important milestone in the development of the caGrid portal focused on the end-user researcher.
This release provides a large catalog of caBIG®-related items that can be browsed quickly to identify the key data sets, institutions, queries, communities, individuals, tools and analytic and data services. There is a sophisticated search through these items that allows users to rapidly find the information they need. The caGrid portal now allows users to create ad-hoc communities around any aspect of the portal. There are many tools available in the new Portal. The existing tools such as the caBIO portlet are still available with minor enhanced functionality. Shared queries have been significantly enhanced. Features are presented in a new cleaner looking, simpler interface.
- CTCAE 4 Governance Document available
Announced March 19, 2010
A document describing the Governance process for CTCAE 4 is available for download at this site: CTCAE 4 and Documentation. CTCAE 4.02 itself is also available for download in multiple formats from this location.
- NCI BioPortal will retire in June
Announced March 19, 2010
NCI BioPortal is scheduled for retirement on or around June 18, 2010. The new NCI Term Browser now provides all sources and most of the functionality that was provided by BioPortal. The term browser has better performance and a more user friendly user interface. If there are any users or applications utilizing BioPortal that cannot transition to Term Browser by this date, please send an email to firstname.lastname@example.org as soon as possible.
- ECCF Training Materials
Announced March 3, 2010
The materials presented at the ECCF training course on February 24-25, 2010 have been released. Updates to these materials will be published over the next few weeks. Please visit ECCF Training Materials for details.
- How To Contribute To LexEVS
Announced March 3, 2010
Have you created an extension or feature which enhances your use of LexEVS? With the migration of the LexEVS source code to ncisvn, this open source project is now prepared to accept your contributions to this tool. Please visit the How To Contribute To LexEVS to learn more.
- IHTSDO Workbench Online Training (Webinar)
Announced March 11, 2010
A new release of the IHTSDO Workbench is due to be released shortly. This Workbench is used for authoring SNOMED CT. Contained in this release is functionality used to create, review and automatically populate refsets using pre-efined queries. This webinar will demonstrate how the Workbench can be used to create refset specifications, compute refset members, allow refsets to be reviewed, and also show how refsets can be used to refine search results. It is free of charge and is scheduled for 1600 UTC on the 11th March and can be booked using this link.
- caGrid release openMDR 1.0
Announced February 25, 2010
The openMDR team is pleased to announce the release of OpenMDR version 1.0. OpenMDR is a suite of software that provides caGrid-compatible semantic metadata management capabilities. The suite includes four different components.
In summary, MDR Core is a semantic repository. MDR Query is a grid service used to search multiple semantic repositories (including MDR Core). UML modelers use MDR Plugin to search for semantic concepts from within Enterprise Architect. caGrid Service Developers use the MDR Domain Model Generator to create caGrid data services.
For more information start at the openMDR overview.
- Sunset of LexEVS 4.0 and 4.1
Announced February 1, 2010
Due to the release of LexEVS 5.1, the subject versions of LexEVS will be retired. Please contact the Vocabulary Knowledge Center if you will not be able to transition to the new version before February 1, 2010.
We are also planning to retire LexBIG 4.2 sometime this spring. April is the target. If you will not be able to transition off of LexBIG 4.2 in that timeframe please let us know soon.
- CDISC CSHARE Demonstrations
Announced December 2 & 16, 2009
Thank you to everyone who has attended the two recent demonstrations of the CDISC CSHARE application. For demonstration and presentation materials and to access the demo site please go to CDISC Shared Health and Clinical Research Electronic Library (CSHARE).
- Two challenge grants have been funded that will build upon cTAKES, Mayo Clinic's Clinical Text Analysis and Knowledge Extraction System, released through the Open Health Natural Language Processing Consortium (OHNLP) in March 2009.
Announced December 3, 2009
The first project, "Natural Language Processing for Cancer Research Network Surveillance Studies" launches a collaborative effort to advance adoption within the HMO Cancer Research Network (CRN) of "industrial-strength" natural language processing systems.
The second project, "Multi-source Clinical Question Answering System" proposes to develop a unified platform for clinical Question Answering (QA) from multiple sources of clinical and biomedical narrative that implements semantic processing of the questions by fusing two existing technologies - Mayo Clinic's cTAKES (Clinical Text Analysis and Knowledge Extraction System) and the University of Colorado's Question Answering System.
- caCORE 3.x APIs and all related grid services were decommissioned
Announced August 7, 2009
After the decommissioning, all applications that use the caCORE 3.x APIs and the grid services listed below, will no longer work. Please visit the decommission page to find out details and suggested solutions.
- SMW 1.4.2 released
Announced February 11, 2009
The SMW Project provides the second update for SMW 1.4. The new version includes a number of changes such as significant performance improvements, initial PostgreSQL support, and a new JSON data export. Also, the query formats vCard and iCalendar have been moved to Semantic Result Formats 1.4.2, so it is wise to update both extensions at the same time. Other than this, upgrade is very easy, see Installation 1.4.2 for details. Further information is found on the SMW 1.4.2 page.