User talk:Jgrethe

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Your edits
Hi -- I'm trying to understand what you're hoping to accomplish. As a neuroscientist myself, I'm all in favor of bringing informatics into play, but there are some problems with your approach. The articles you've created, Neuroscience Information Framework and NeuroLex, seem to consist largely of material copied directly from copyrighted web pages, and I can't see any evidence that you have permission to do that. Also, I think the NeuroLex system needs to achieve some level of notability in the neuroscience community before it is used for articles like Purkinje cell, and I haven't seen any evidence of that either. I'm not trying to be hostile -- I see now reason not to have articles on NIF and NeuroLex -- but we have to do things the right way. Could you give me some feedback on this? Regards, Looie496 (talk) 19:29, 7 April 2009 (UTC)

Re: Your edits
Hi Looie496, First, perhaps a bit of background. The NeuroLex terminology is part of a project (NIF) that is funded by NIH's Neuroscience Blueprint. The primary goal is to provide an enhanced search portal for the neuroscientist to discover data and information from resources that are many times not easily discovered via current search technologies (e.g. databases and form based web sites that are sometimes referred to as the hidden or deep web). A core part of enabling such an infrastructure is the utilization of domain specific terminologies/ontologies. NeuroLex is the part of the project that looks to bring such terminologies together - that is, NeuroLex isn't building a completely new terminology. Rather it is incorporating open source terminologies when available and developing/updating terminologies where content is not available. For example, terminology related to brain regions is covered in a variety of sources. In NeuroLex (http://neurolex.org/wiki/Category:Cerebellum) we have incorporated the terminology from various sources and formalized this in OWL (Web Ontology Language) while maintaining all the links and references to the source terminologies (e.g. NeuroNames, UMLS, etc...). The use of such ontologies is important in the development of many "semantic" applications. For example, when searching for gene expression in the cerebellum - what should you search for: cerebellum, Purkinje Cell layer, Dentate, etc... By having an ontology, we can then automate this "expansion" of the search to include all relevant "parts-of" the cerebellum.

In regards to your comments above:
 * what you're hoping to accomplish
 * As mentioned above, in building NeuroLex we provide links back to the source terminology that we have incorporated. We are beginning this process with Wikipedia right now - provide links from NeuroLex to Wikipedia and vice versa. That is why I structured the external links section that way that I did -  I can actually envision other ontology efforts placing similar links to their ontology content and the "Semantic" heading provides a place for such links to be added without interfering with the rest of the article.
 * NeuroLex is built on MediaWiki with Semantic Media Wiki extensions - allowing the research community to define formal relationships and attributes on terms (e.g. Purkinje Cell is located in Purkinje Cell Layer which is located in Cerebellum) that can be incorporated in formal ontologies.
 * I'm all in favor of bringing informatics into play, but there are some problems with your approach
 * Not sure how to answer here - as there are many approaches depending on the desired utilization of a terminology.
 * The articles you've created, Neuroscience Information Framework and NeuroLex, seem to consist largely of material copied directly from copyrighted web pages
 * I am Co-Principal investigator on the NIF project and we utilized some of the same overview text to get the articles started.
 * More generally, in terms of use and access, all services and terminologies that NIF develops are being made freely available. NeuroLex is available for download from multiple sources and can be freely re-used and re-purposed (Creative Commons license).
 * NeuroLex system needs to achieve some level of notability in the neuroscience community before it is used for articles like Purkinje cell
 * NeuroLex is a formal ontology that has a level of notability:
 * Is called out in current Challenge Grants
 * 06-DA-109 Developing new computational approaches to Information Retrieval. Development of computational approaches which query multiple data sources and types relevant to basic neuroscience and behavioral addiction research, and which (1) employ or add to the Neurolex vocabulary (http://www.neurolex.org) of the NIH Blueprint Neuroscience Information Framework and (2) focus on enabling user-friendly complex queries based on concepts, anatomical coordinates, and other query parameters relevant to addiction research, that return source data elements directly within a format and context that makes them easily interpreted and accessible.
 * Was originally developed as part of activities within the Biomedical Informatics Research Network (funded by NIH) - the neuroscience specific component (NeuroLex) is now hosted by the NIF project
 * We have been working closely with the National Center for Biomedical Ontologies (an NIH funded National Center for Biomedical Computation) and NeuroLex been submitted to be made available through their BioPortal as well (in addition to the free download from the NeuroLex PURL http://purl.org/nif/ontology/nif.owl).
 * Is utilized by numerous research groups in the U.S. and Europe

Hopefully, this answers your questions (sorry about the length). If you have any other questions just post back... Jgrethe (talk) 23:57, 7 April 2009 (UTC)


 * The immediate problem is that the web pages say "All rights reserved", and putting the material on Wikipedia violates that. If you have rights over the web pages, there are several ways you can deal with this, see Donating copyrighted materials for an explanation of all the details.  It's essential to get this right, because the survival of Wikipedia depends on rigorously respecting copyright law.  The lesser issue, which is open to discussion, is that my personal feeling is that the system shouldn't be used outside the articles devoted to it until it has been described in a peer-reviewed publication.  Regards, Looie496 (talk) 01:14, 8 April 2009 (UTC)

Re: Your edits
Hi Looie496, Which page says 'All rights reserved'? The NeuroLex pages state 'Content is available under BSD License' and show the creative commons license with the link to the license. The parent project's website (NIF) just has the standard copyright on the bottom (which is not really needed anyway since anything that is 'created/published' immediately has copyright protection'. So I am not sure where you see that...  If you can point me at the offending page I can look into, and get it corrected, as all NeuroLex content is being made available through the Creative Commons license.  THank you for your help in tracking this down! 137.110.111.249 (talk) 16:27, 8 April 2009 (UTC)
 * Hmm -- the NeuroLex website seems to have been hijacked at the moment -- after a delay of a couple of seconds I am being redirected to a .tv site. Looie496 (talk) 17:45, 8 April 2009 (UTC)
 * Following up, regardless of the type of copyright any copied material in an article needs to be attributed explicitly to its source -- not necessarily legally, but by Wikipedia rules so that an editor can determine the status of the material. I may have been wrong about the "all rights reserved", but in any case even a "standard" copyright doesn't grant the right to copy beyond fair use, so that needs to be made explicit. Looie496 (talk) 17:59, 8 April 2009 (UTC)

Re: Re: Your edits
Hi Looie496, Thanks for the information. I can add the attribution to the pages (again these are being made available via a Creative Commons license and I can add that). Jgrethe (talk) 21:59, 9 April 2009 (UTC)

April 2009
Welcome to Wikipedia. Although everyone is welcome to contribute constructively to the encyclopedia, one or more of the external links you added do not comply with our guidelines for external links and have been removed. Wikipedia is not a collection of links; nor should it be used for advertising or promotion. Since Wikipedia uses nofollow tags, external links do not alter search engine rankings. If you feel the link should be added to the article, please discuss it on the before reinserting it. Please take a look at the welcome page to learn more about contributing to this encyclopedia. Dicklyon (talk) 15:12, 21 April 2009 (UTC)

Template edits
Hi -- I just wanted to say that the changes to the neuron infobox look great. Looie496 (talk) 16:31, 17 May 2009 (UTC)

Hi Looie496 -- Thanks... I tried to make some minor updates to make this infobox similar to the brain infobox. I also updated the documentation as that was woefully lacking. Jgrethe (talk) 21:52, 18 May 2009 (UTC)

Welcome to SfN project
I noticed you added the SfN initiative userbox, and I just wanted to say welcome! --Tryptofish (talk) 19:23, 28 July 2009 (UTC)