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Report from the Field: NIF in the lab

This report discusses significant successes and challenges encountered in utilizing the NIF (Neuroscience Information Framework) for data federation, gene homolog exploration, and literature integration. It highlights the streamlined processes for searching and exporting results, detailing advancements in semantic enhancement and the importance of tailored queries for complex questions. It also addresses difficulties faced in accessing literature off-campus and suggests improvements for user contributions to enhance the semantic search experience within the NIF ecosystem.

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Report from the Field: NIF in the lab

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  1. Report from the Field:NIF in the lab Jonathan Cachat NIF AHM May 31, 2012

  2. Successes • Data Federation • Gene Homologs – search once, export results

  3. Data Federation

  4. Successes • Data Federation • Gene Homologs – search once, export results • Signaling Networks –single site = all information • However; requires very specific question to be answered • Should this be initial landing page? Can it be customized using myNIF?

  5. Successes • Data Federation • Gene Homologs – search once, export results • NIF Registry • Finding software/analysis tools

  6. NIF Registry

  7. Successes • Data Federation • Gene Homologs – search once, export results • NIF Registry • Finding software/analysis tools • Literature • Novel perspective on literature landscape • Semantic Enhancement – to a point • Its amazing what can be missed by remaining at PubMed

  8. Difficulties • Literature • Get PDF using university/institutional credentials – when off campus (~50%) (i.e. PubGet) • Reference Management and Annotation software integration • Semantic Enhancement • Excellent with Neurons, Human/Rodent brain regions • However, broad terminology (i.e. animal behavioral tests) not really supported – easy to contribute, but where? Behavioral Paradigm Hierarchy = Human • Not tailored for “my domain” & unclear how to easily contribute….

  9. Ex: Zebrafish Genes ? ?

  10. Ex: Zebrafish Brain Regions Mueller, T. (2012). What is the Thalamus in Zebrafish. Front Neurosci. doi:10.3389/fnins.2012.00064 Friedrich, R. W., Jacobson, G. A., & Zhu, P. (2010). Circuit Neuroscience in Zebrafish. Current Biology, 20(8), R371–R381. doi:10.1016/j.cub.2010.02.039

  11. and more complicated…..

  12. Suggestions • myNIF Integration w/ Search Interface • Save Results • Add Literature to myNIF Library • Also, added data to formulate “interest cloud” • More clear “contribute” mechanisms to modify and enhance semantic search w/ faster turn around – “I” have knowledge, let me quickly contribute & have other experts contend

  13. Social Media Brief

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