Report from the Field:NIF in the lab

Jonathan CachatNIF AHM

May 31, 2012

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

Data Federation

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?

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

• NIF Registry– Finding software/analysis tools

NIF Registry

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

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….

Ex: Zebrafish GenesGene Offical Symbol

5htr-1aa htr1aa

5htr-1ab htr1ab

5htr-1b LOC561647

5htr-1bd htr1bd

?

?

Ex: Zebrafish Brain Regions

Mueller, T. (2012). What is the Thalamus in Zebrafish. Front Neurosci. doi:10.3389/fnins.2012.00064Friedrich, 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

Zebrafish to Mammalian Brain Region HomologiesZebrafish Mammalian

Optic tectum Superior colliculusPars ventralis Subpallium (striatum, pallidum, and septum)Pars dorsalis Pallium (cortical structures)Dp in lateral pallium Paleocortex (olfactory cortex)Dlv in medial pallium HippocampusDm in ventral pallium AmygdalaVv/Vl of ventral telencephalon Septal formationVc/Vd of ventral telencephalon Striatum/Pallidum

and more complicated…..

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

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