# Presentation: 453407

## NIF Literature Search Engine

**Much information are details hidden in the full text, and **
**are neither in the abstract nor captured in MeSH terms.**

**We designed Textpresso to do automated skimming      for researchers and database curators.**
**The output can be used for more sophisticated       ****N****atural ****L****anguage ****P****rocessing.**

**www.textpresso.org/neuroscience**

**NIF Literature Search Engine**

## Full Text

**Sentence**

**Ontology**

**PubMed**

**Google Scholar**

**(-)**

**+**

**+**

**+**

**-**

**-**

**-**

**MeSH**
**Taxonomy**

**NIF standard**
**Gene Ontology**
**customized**

**Textpresso**

**Can we do better than PubMed and Google Scholar?**

## BRAIN

- upstream           cascade
-       descendants

**Polycystin 1**

**BRAIN**
**AREA**

- FOXO
-           HOXA1
-            pax2
- PKD1

**          **SCN
- CA3
-         cortex

- Polycystic kidney disease 1 PKD1 UGID:139915 139915  NP_038658.1  UniGene Hs.75813  NM_000296.2  CR613181.1  U24497.1  AB209675.1

**NIF provides vocabulary**

***Categories are “bags of words”***

## Individual sentences in full text are marked up with Categories

**TEXTPRESSO CATEGORIES**

***Individual sentences in full text are marked up with Categories***

- Automatically mark up the whole corpus of papers with terms of categories,                        and index for rapid searching

## Example 1

- Specify categories “(NIF) cell types” _and_ “brain area” _and_ “TRP channel”

***Are there any cell types in specific brain areas that are somehow associated with TRP channels?***

## Some answers to Example 1

**from ~15,000 papers in NIF pilot**

## 2. Is a nicotinic receptor associated with 

_**Drugs of Abuse**_** other than **_**nicotine**_**?**

## 3. Are NICSNP candidate genes involved in regulation of, or by, receptor/second messenger signal transduction?

**3. Are **_**NICSNP candidate genes**_** involved in **_**regulation**_** of, or by, **_**receptor**_**/**_**second messenger**_** signal transduction?**

## Textpresso for NIF vocabulary development

**Textpresso for NIF vocabulary development**

**Natural Language Processing algorithms:**
**	****entity recognition by Word Sense Disambiguation**
**	****now used to recognize Drosophila gene names **
**	****	****	****(“not”, “We”, “yellow”, ...)**
**	****future: capture new cell types, databases, genes, etc.**

## 100 sentences per hour

**	****26,000 sentences out of 4.400 articles**
**simple interface to “check off” sentences**

***Database curation: e.g. Gene-Gene Interactions***

- output into database

## Scaling Textpresso

**15,000**

**30**

**45 Gb**

**150,000**

**300**

**450 Gb**

**1,500,000**

**3,000**

**4.5 Tb**

**15,000,000**

**30,000**

**45 Tb**

**No. papers**

**CPU hours**

**Storage**

**Jan 2008**

**Dec 2007**

- ~neuroscience papers in PubMed

- ~papers in PubMed

**for indexing**

**some existing systems:**
***C. elegans*****: 9400**
**yeast: 40,000**
**Drosophila: 20,000**

## Full Text

**Sentence**

**Ontology**

**PubMed**

**Google Scholar**

**-**

**+**

**+**

**+**

**-**

**-**

**-**

**MeSH**
**Taxonomy**

**NIF standard**
**GO**
**customized**

**Textpresso**

**Ontology + Sentence level scope ****	****	****Semantic Queries**

**Comparison to PubMed and Google Scholar**

## www.textpresso.org

***Caltech Team:***
**Hans-Michael Müller****, ****Arun Rangarajan,Tracy Teal**
**Kimberly Van Auken, Juancarlos Chan,**
**Weiwei Zhong**
**Paul Sternberg**

**www.textpresso.org**

**Textpresso is a stand alone, open source system that is accessed by Neuroscience Information Framework (NF) via webservices. Textpresso is used by the model organism databases WormBase, FlyBase and SGD (yeast), and is being developed for TAIR (Arabidopsis) and others.  Also used by vaccine database Violinet.  **

## List of Journals for Neuroscience

- BMC Neurosci
- Nat Rev Neurosci
- J Neurosci
- Nat Neurosci
- Neuron
- Neuroscience
- J Neurophysiol
- Exp Brain Res
- Curr Opin Neurobiol

- Brain Res
- Trends Neurosci
- Cereb Cortex
- Annu Rev Neurosci
- Int J Neurosci
- Int Rev Neurobiol
- J Comp Neurol
- Eur J Neurosci
- Neurobiology

## Slide 15

## gene A mouse

**Zhong & Sternberg *****Science 2006***

**phenotype**

**expression**

**Gene Ontology**

**interacting genes**

**gene A mouse**

**What is known about a particular gene from model organisms?**

**John Satterlee’s use case:**

**{mouse, worm, fly}                mouse, worm, fly, fish, yeast, slime mold}**

## www.geneorienteer.org

**www.geneorienteer.org**

## www.geneorienteer.org

**www.geneorienteer.org**

## www.geneorienteer.org

**www.geneorienteer.org**

## Slide 20

## What specific C. elegans cells have been used for huntingtin studies using reporter genes? [search all 9400 C. elegans papers]

## identifies:    sensory neurons, ASH neuron, muscle

**identifies:    sensory neurons, ASH neuron, muscle**
**	****	****GFP, YFP**

**What specific *****C. elegans***** cells have been used for huntingtin studies using reporter genes?**

## Textpresso for Neuroscience: Example 2

- Enter categories “drugs of abuse”, “brain area” and “NIF cell type”.

***What cell types in what brain areas are associated with substances of abuse?***

## Slide 24

## 2. Curation Pipeline: Textpresso for GO 

**Cellular Component Annotations**

**Weekly search of new *****C. elegans***** papers**
**with CCC categories returns sentences from ~10 – 15 papers**

**Further supporting these conclusions, ****GFP-tagged**** ****CMD-1**** does not ****accumulate**** at the furrow, but does ****accumulate**** on the ****spindle**** and ****centrosomes**** (as well as to the interphase ****nuclear membrane**** and the borders of abutting cells) (Fig 3 and Supplementary Video 2).**
***Cytokinesis is not controlled by calmodulin or myosin light chain kinase in the Caenorhabditis elegans early embryo. *****Batchelder EL, Thomas-Virnig CL, Hardin JD, and White JG. FEBS Lett. 2007 Sep 4; 581 (22): 4337-41.**

## Portal to Neuroscience Literature

***Portal to Neuroscience Literature***