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Free engine to datamine Pubmed for relationships


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#1 opales

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Posted 28 October 2006 - 10:59 AM


This reminds me of Biomind's Bioliterate (Bruce Klein has been working on that I think). I remember Ben Goertzel mentioning something like that within 10 years all biologist will be using these tools because incredible amount of information out there. Anyway, it's better to be an early adopter, especially in something that appears as useful as this:

http://www.chilibot.net/

Mining PubMed for relationships

Chilibot searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords. The results are returned as a graph (see examples). We support several different search methods.



Here is an example of using keywords

sir-2 and aging

SIR-2 & AGING

Retrieving synonyms..

Retrieving abstracts .. |SIR-2/AGING ..................................................
Performing linguistic analysis ..
. Abstracts found: 86| Abstracts analyzed: 50 (most recent)
Interactive relationship (e.g. stimulation, inhibition, etc)

# SIR2 [SIR-2] is a key regulator of the aging process in many model organisms. Ref: J Biol Chem, 2005

# Sir2 [SIR-2] and insulin IGF 1 are the major pathways that impinge upon aging in lower organisms. Ref: PLoS Biol, 2006

# The NAD dependent histone deacetylase Sir2 [SIR-2] plays a key role in connecting cellular metabolism with gene silencing and aging. Ref: Mol Cell Biol, 2006

# Members of the Sir2 [SIR-2] family of NAD dependent protein deacetylases regulate diverse cellular processes including aging, gene silencing, and cellular differentiation. Ref: J Biol Chem, 2005

# C. elegans SIR 2 [SIR-2] .1, a member of the Sir 2 [SIR-2] family of NAD ( ) dependent protein deacetylases, has been shown to regulate nematode aging via the insulin IGF pathway transcription factor daf 16. Ref: Dev Cell, 2005

# SIR2 [SIR-2] genes control life span in model organisms, playing a central role in evolutionarily conserved pathways of aging and longevity. Ref: Genomics, 2005

# We found that aging in DeltaNp63alpha transgenic mice and other mouse models correlated with levels of Sirt1, a mammalian SIR2 [SIR-2] orthologue thought to extend the lifespan in lower species. Ref: Cell Cycle, 2006

# Silent Information Regulator 2 ( Sir2 [SIR-2] ) enzymes ( or sirtuins ) are NAD ( ) dependent deacetylases that modulate gene silencing, aging and energy metabolism. Ref: Proc Natl Acad Sci U S A, 2006

# The demonstrated roles of SIRT1, the mammalian counterpart of the yeast SIR2 [SIR-2] , reveal that SIRT1 regulates important cellular processes including anti apoptosis, neuronal protection, cellular senescence, aging and longevity. Ref: Med Hypotheses, 2006

# , 2006 ) reports that deficiency in one of the mammalian Sir2 [SIR-2] homologs, SIRT6, results in genome instability through the DNA base excision repair pathway and leads to aging associated degenerative phenotypes. Ref: Cell Metab, 2006

# Silent information regulator 2 ( Sir2 [SIR-2] ) proteins are a class of protein deacetylase enzymes that play key roles in transcriptional gene silencing, DNA repair, and aging. Ref: Protein Expr Purif, 2006

# The null mutation of the SIR2 [SIR-2] gene in Saccharomyces cerevisiae has been associated with a series of different phenotypes including loss of transcriptional silencing, genome instability and replicative aging. Ref: Nucleic Acids Res, 2006

# SIR2 [SIR-2] and its mammalian derivatives play a central role in epigenetic gene silencing, recombination, metabolism, cell differentiation and in the regulation of aging. Ref: Int J Oncol, 2006

# SIR2 [SIR-2] and its mammalian orthologs play an important role in epigenetic gene silencing, DNA recombination, cellular differentiation and metabolism, and the regulation of aging. Ref: Int J Oncol, 2006

# In addition, stress response pathways and mitochondrial mechanisms, dietary restriction, SIR2 [SIR-2] deacetylase activity, TOR and TUBBY signaling, as well as telomere length contribution are discussed in relation to recent developments in C. elegans aging research. Ref: Exp Gerontol, 2006

# The Silent information regulator2 ( Sir2 [SIR-2] ) family of proteins ( sirtuins or SIRT ) which belong to class III histone protein deacetylases, have been implicated in calorie restriction, aging and inflammation. Ref: Am J Physiol Lung Cell Mol Physiol, 2006

# ABSTRACT BACKGROUND During the last two decades progress in the genetics of aging in invertebrate models such as C. elegans and D. melanogaster has clearly demonstrated the existence of regulatory pathways that control the rate of aging in these organisms, such as the insulin like pathway, the Jun kinase pathway and the Sir2 [SIR-2] deacetylase pathway. Ref: BMC Genomics, 2006

# Yeast Sir2 [SIR-2] is a nicotinamide adenine dinucleotide ( NAD ) dependent histone deacetylase that plays a central role in transcriptional silencing, chromosomal stability, DNA damage response and aging. Ref: Genes Cells, 2005

# The evolutionarily conserved Sir2 [SIR-2] protein family requires NAD for its deacetylase activity and regulates a variety of biological processes, such as stress response, differentiation, metabolism, and aging. Ref: J Biol Chem, 2004

# The yeast Sir2 [SIR-2] protein and its mammalian derivatives play a central role in epigenetic gene silencing, DNA repair and recombination, cell cycle, microtubule organization, and in the regulation of aging. Ref: Int J Oncol, 2005

# The yeast Sir2 [SIR-2] protein and its mammalian derivatives play a central role in epigenetic gene silencing, DNA repair and recombination, cell cycle, microtubule organization, and in the regulation of aging. Ref: Int J Mol Med, 2006

# Sirtuin 5 ( SIRT5 ) is a nicotinamide adenine dinucleotide ( NAD ) dependent deacetylase and belongs to the Silent information regulator 2 ( Sir2 [SIR-2] ) family of sirtuin histone deacetylases ( HDACs ), which play a central role in epigenetic gene silencing, DNA repair and recombination, cell cycle, microtubule organization, and in the regulation of aging. Ref: Cytogenet Genome Res, 2006

# In contrast to measurements of aging for mitotic cells, cell survival in the nonmitotic state is decreased by Sir2 [SIR-2] activity under conditions that mimic calorie restriction. Ref: Cell, 2005

# In yeast, Sir2 [SIR-2] is required for maintaining replicative life span, and increasing Sir2 [SIR-2] dosage can delay replicative aging. Ref: Cell, 2005

# Sir2 [SIR-2] is also implicated in the regulation of aging, because its increased expression extends the lifespan of yeast and nematodes. Ref: J Pharmacol Sci, 2005

Parallel relationship (e.g. studied together, co-existance, homology, etc.)

# Among many genes thus far reported contributing to aging process, the yeast silent information regulator 2 ( SIR2 [SIR-2] ) and its homologues in other species, which belong to the family of type III histone and protein deacetylases, have been the subject of active discussion. Ref: Med Hypotheses, 2006

# The enigmatic role of Sir2 [SIR-2] in aging. Ref: Cell, 2005

# We also evaluated two molecules implicated in the pathophysiology of aging, p53 and silent inflammatory regulator 2 ( Sir2 [SIR-2] ). Ref: Diabetes, 2006

# Sir2 [SIR-2] NAD dependent deacetylases connect transcription, metabolism, and aging. Ref: Cell Metab, 2005

# We review Sir2 [SIR-2] , a factor linking genomic stability, metabolism, and aging. Ref: Cell, 2005

# , 2005 ) examine the role of Sir2 [SIR-2] , a histone deacetylase, in chronological aging in yeast by measuring the long term survival of nondividing cells. Ref: Cell, 2005

# The Sir2 [SIR-2] histone deacetylase functions as a chromatin silencer to regulate recombination, genomic stability, and aging in budding yeast. Ref: Cell, 2006

# In yeast, a mechanistic explanation has been proposed whereby calorie restriction slows aging by activating Sir2 [SIR-2] . Ref: PLoS Biol, 2004


Edited by opales, 28 October 2006 - 11:15 AM.

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#2 Logic

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Posted 04 April 2015 - 09:29 AM

I'm surprised at the lack of response to this post?

This is a great piece of software for joining the dots.

 



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#3 Antonio2014

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Posted 04 April 2015 - 10:45 AM

I remember Ben Goertzel mentioning something like that within 10 years all biologist will be using these tools because incredible amount of information out there.

 

Now that almost 10 years have passed, are they using them?


Edited by Antonio2014, 04 April 2015 - 10:47 AM.


#4 Kalliste

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Posted 04 April 2015 - 12:29 PM

A lot of AI researchers are still working in this direction but many projects are not speaking out very much at all. And when they do, they are often horribly disfigured in the details of their work by the pop-sci press.



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#5 DonManley

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Posted 19 April 2015 - 08:59 PM

I think if people were to put information in another format, it would be easier to read both by humans and by machines. I doubt natural language is the best way to store information. Graphs can describe complex relationships between data and present it to humans in a more brain-friendly way as well as to machines. It's much easier to look at a mindmap and understand the big picture than it is by reading an academic text. Why not just input most information as a structured mindmap / graph and then also expose your empirical / statistical data? There are some new classes of databases coming out like datomic, which can store information as a bunch of facts, you can even easily query that information against time, e.g., check what was the knowledge year ago or a month ago. It's also good for AIs, because one can e.g. feed AI information from a year ago to train it and then check how well it performs using information from this year. But the most important feature I think is that it's theoretically possible to maintain multiple versions of the same graph without duplicating data. Imagine being able to fork all knowledge in an instant and then add your own data to it. It can act like git for knowledge. And, of course, graphs are extremely good for querying relationship between nodes. I hope something like this will become an option in the future and we'll have structured knowledge (in contrast to knowledge stored as a natural language, like publications or wikipedia).

 

Meanwhile, there are some sites like: http://examine.com/s...ents/Magnesium/which attempt to give a structured summary of a substance, its general effects on human body, list of studies that explore those effects; as well attempt to quantify how reliable that information and whether there is scientific consensus.

 

Of course, AI that can deduce that information from natural language is much more promising. Speaking of which, Watson, the AI that defeated humans on Jeopardy, is now learning medical data. I haven't been following its progress lately, but it seems that they already made pretty cool applications for it like WatsonPaths, which "can examine the scenario from many angles, working its way through chains of evidence – pulling from reference materials, clinical guidelines and medical journals in real-time – and drawing inferences to support or refute a set of hypotheses."

 

IBM also announced the Watson Health project:
 

 

IBM Watson Health will develop an online database of constantly updated, anonymised health information collected from many sources, including health apps used by Apple customers and fitness devices.

The database "will enable doctors and researchers to draw on real-time insights from consumer health and behavioral data at a scale never before possible", John E. Kelly, a senior vice president at IBM, said in a statement.

 

 


Edited by DonManley, 19 April 2015 - 09:03 PM.





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