Archive for the ‘Jonathan Cachat’ Category

Neuronal Computation Series – NIF Webinars

Posted on September 24th, 2013 in Jonathan Cachat, Webinar Announcement | No Comments »

October will kick off a NIF webinar series around the topic of Neuronal Computation. What is that you ask?

Three rather remarkable and ambitious projects will be highlighted:

On October 1st, Stephen Larson will be discussing the Open Worm Project

Open Worm Project


October 15th, Kenneth Yoshimoto will be presenting on the Neuroscience Gateway Portal


and October 29th, Padraig Gleeson will be presenting on the Open Source Brain initiative.


 check out the full details and descriptions here

We look forward to seeing you there. Also please feel free to contact us – or @neuinfo - with any feedback, comments or webinar suggestions.

BioCreative User Interactive Task – Request

Posted on September 4th, 2013 in General information, Jonathan Cachat, Maryann Martone, News & Events | No Comments »

The Neuroscience Information Framework is proud to support the BioCreative effort ( whose goal is bridging the gap between text mining and biocuration.

One activity BioCreative is currently recruiting for is a User Interactive Task (IAT) where a domain expert for a biocuration task is recruited to test a system.

This study is conducted remotely and is time flexible, as long as the evaluation is performed by September 25.  There are two levels of participation: full (involves actual curation of a selected corpus (about 60 abstracts total), completing a user survey, and being listed as co-author on the BioCreative IAT overview article) and partial (involves performing basic pre-defined tasks at the system’s website, completing a user survey and being acknowledge in the BioCreative IAT overview article).

BioCreative has 9 systems and one of them is EGAS (, a web-based platform for biomedical text mining and collaborative curation, supporting manual and automatic annotation of concepts and relations. In this case related to protein interactions in biomedical corpus related to neurological diseases.

Since NIF’s community expertise is on neurosciences BioCreative wanted to ask for our help to recruit suitable participants. Specially, they are in need for a couple of participants for full testing of EGAS.

The benefits to biocurators participating in this activity are multifold, including:

  • direct communication and interaction with developers
  • exposure to new text mining tools that can be potentially adapted and integrated into the biocuration workflow
  • contribution to the development of text mining systems that meet the needs of the biocuration community
  • dissemination of findings in a peer-reviewed journal article.

Here is the website for BioCreative IAT:

Link to EGAS system and task description:

To register, select EGAS as the system in the registration page:

We have A LOT of neuroscience information, and would like to share….

Posted on May 14th, 2013 in Curation, Inside NIF, Jonathan Cachat | No Comments »

Over the past 4 years, the Neuroscience Information Framework systematically scanned the literature, internet and social buzz for all things neuroscience (& biomedical science). This tedious bookkeeping has resulted in the largest, most comprehensive catalog of neuroscience-relevant information ever amassed – with the added bonus of semantically enhanced search functions. And now, we would like to share it with you via myNIF…but before those details…

What do we mean “neuroscience information”?

Neuroscience information includes data, resources, literature, grants, multimedia, social buzz, a lexicon and more..

Data: Over 140 independent databases (i.e. CCDB,, GENSAT) are deeply indexed and semantically mapped by NIF – representing over 400 million pieces of data. These data are considered part of the “hidden web”, not indexed by major search engines because do so requires specialized database query statements for retrieving data within, rather than on the surfaces of pages surrounding the database. NIF has developed technologies to regularly re-crawl and update data content, index it, and provide search within the contents of these databases simultaneously. Moreover, data resulting from a search can be exported with a single click into standard data formats for desired, subsequent analysis. This can simply save  you time – if you need to know what type of serotonin receptors have been classified in zebrafish (Danio rerio) – searching NIF for ‘zebrafish serotonin receptor’ provides results from authoritative data providers (HomoloGene, EntrezGene) which can be compared instantly, rather than visiting each site separately, and comparing through notes, multiple windows, or several downloads. In addition to this primary information , the results also include related, and sometimes very helpful information about zebrafish and serotonin – signaling pathways, antibodies, and grant information.

Resources: Need to find a software analysis package for microarray data? NIF can recommend 41 options, as well as 100+ unique organizations, centers, labs and websites that  have similar interests. Looking for non-governmental funding of ALS research? Here are 7. What about a tissue bank with Alzheimer’s disease CNS tissue samples available for researchers? NIF is aware of around 88 worth a look. All of this to convey that a resource is object or entity, with a website, that provides potential value to neuroscience research or the researchers. Importantly, this catalog of resources indexed by NIF is maintained at NeuroLex, a semantic mediawiki website. Homologous to Wikipedia, in that any one can contribute their resource or favorite resources, but endowed with reasoning capabilities permitting logical reasoning on relationships between data (i.e. list all GABAergic Neurons).

Lab Data Management Practices?

Posted on April 28th, 2013 in Force11, Jonathan Cachat, NIFarious Ideas | 2 Comments »

A number of groups, from libraries and universities and academic projects are striving to implement flexible data management systems in order to harness the latest and greatest in semantic web technologies striving to integrate and facilitate breakthrough interdisciplinary analysis.

It is known that every lab, every individual research group (regardless of the discipline) has developed internal data management systems that “work” (i.e. literature & data collection > excel > stats > graphing > word processer) but what has your lab found useful and what are your biggest frustrations?

Please feel free to comment below, or join the discussion on ResearchGate.


A Call to Science Bloggers

Posted on November 9th, 2012 in Force11, Interoperability, Jonathan Cachat, News & Events | 5 Comments »

With the growth of scientist participation in blogging and social networks, a considerable amount of meritable scientific chatter is unfolding online. Several prominent blogs have emerged, in fact NIF is now indexing may of these sites (via RSS feeds) and can be found in the Multimedia data type***.

In our continued effort to integrate and link data, NIF would like to create two-way links between your blog posts and the scientific articles they discuss through NIF Literature. For example, if users find an article in NIF Literature we can provide links to blogs or tweets that have discussed this article, in addition to the current link to full text access options. Your site or blog would also be included on PubMed search results thank’s to NIF automated LinkOut feature services.

However, it is currently very hard to achieve this goal and would require substantial manual curation efforts. In order to automate this process, we submit a few simple guidelines to the online science community.

1) Blogs and other long-form posts should always include related PubMed Identifiers (PMID) in citations. References can be in text, or placed together at the end of a post, but either way should include PMID: ######## for all citations. This standardized format of ‘PMID:######’ was suggested by the BioDBcore and initiatives and we strongly support it.

  • This is a MindHacks post without any citation information at all (aside form a link to Nature) – this is the worst possible scenario, for the purposes of this article. It is a wonderful dialogue on this exciting article, but very unlikely that people reading this article will ever know that this post exists – unfortunate for everyone involved.
  • This Neuroskeptic post correctly included citation information, along with the PMID, at the end of the post (see Screenshot below).

2) Short-form posts should include PMIDs when possible, particularly if linked directly to article. For example a recent tweet here.

3) Be found – index with search engines including NIF. For more information about submitting your site, blog or resource to NIF check here or fill in the small form here.

The internet was designed to enable a web of links between ideas, information and people. Following these simple guidelines will not only increase the connectivity between data, the social and semantic links are also valuable to information creators. First, it promotes more opportunities for scientific exchange and feedback. Secondly, it provides additional avenues to calculate impact metrics – similar to those observed by and PloS Journals.

Do you have any other thoughts related to increasing data integration and interpretability? Share them here in the comments below!

***If you would like to have your blog or site included within the NIF index drop us a line –