GoPubMed: New release

Dear all, http://www.GoPubMed.org is an ontology-based literature
search engine, which can answer questions. We just released a new
version, which integrates biological and medical background knowledge
and offers links to relevant wiki articles and Uniprot entries for
protein names mentioned in the text. Below you find typical questions
relating to Alzheimer, which GoPubMed can answer. If you follow the
example right to the end, you will learn how to treat Alzheimer ;-)

If you like GoPubMed, please tell your friends and help to spread the
word.

Cheers, Michael and the GoPubMed team


Question: Which proteins are related to Alzheimer
Question: Was abeta42 already used in a clinical setting?
Question: Were there clinical trials focussing on Abeta42 and were
any side effects observed?
Question: Which neurons are relevant in Alzheimer?
Question: Which ion channels do CA1 pyramidal neurons have?
Question: Are there antibodies for ADDL?
Question: What treatments does the web offer for Alzheimer?



Question: Which proteins are related to Alzheimer

Answer: Type in alzheimer and open chemicals and drugs in "top five &
more" on the left. Among others there are "Amyloid", "Amyloid
beta-Protein", "Cholinesterase Inhibitors" listed as related proteins.

Clicking on amyloid beta protein, we can reduce from 1000 to 60
relevant articles and get the following definition:

    A 4-kDa protein, 39-43 amino acids long, expressed by a gene
    located on chromosome 21. It is the major protein subunit of the
    vascular and plaque amyloid filaments in individuals with
    Alzheimer's disease and in aged individuals with trisomy 21 (DOWN
    SYNDROME). The protein is found predominantly in the nervous
    system, but there have been reports of its presence in non-neural
    tissue

The second article in the results page mentions e.g. "Inhibition of
aggregation of amyloid p-protein (AP) ... are known as potent
therapeutic tools for Alzheimer's disease (AD)". Another article
states "Reportedly, beta-amyloid peptides (Abeta40 and Abeta42) induce
the neurodegenerative changes of Alzheimer's disease (AD)".


Question: Was abeta42 already used in a clinical setting?

Answer: Type abeta42 drug and go to hierarchy of contents on the left.
Open "chemicals and drugs" and "organic chemicals".  Clicking
"hydrocarbons" results in only 41 articles. Quickly skimming over
them, one sees statements like "minocycline treatment did not alter
the cerebral deposition of Abeta" or "naproxen that do not lower
Abeta42". So, let's move to the next category, carboxylic
acids. Clicking the term displays 36 articles with statements such as
"ibuprofen possess preferential Abeta42-lowering activity".


Question: Were there clinical trials focussing on Abeta42 and were
any side effects observed?

Answer: Type abeta42 clinical trials. In "top five & more" open 
"diseases" and click on "meningoencephalitis".  Four articles are 
returned, such as "subacute meningoencephalitis in a subset of patients 
with AD after Abeta42 immunization." So, there are indeed side effects.


Question: Which neurons are relevant in Alzheimer?

Answer: Type alzheimer neuron and go to "hierarchy of content". Open
anatomy, cells, neurons and you will find pyramidal cells. Hovering
the mouse over the term, gives the explanation:

    Projection neurons in the cerebral cortex and the
    hippocampus. Pyramidal cells have a pyramid-shaped soma with the
    apex and an apical dendrite pointed toward the pial surface and
    other dendrites and an axon emerging from the base. The axons may
    have local collaterals but also project outside their cortical
    region.


Question: Which ion channels do CA1 pyramidal neurons have?

Answer: Type CA1 pyramidal neurons and go to hierarchy of content.
Open chemicals and drugs, amino acids..., proteins, membrane proteins,
membrane transport proteins, and ion channels. Potassium channels are
listed first and clicking returns some 50 papers including e.g. "BK
potassium channels facilitate high-frequency firing and cause early
spike frequency adaptation in rat CA1 hippocampal pyramidal cells".



Question: Are there antibodies for ADDL?

Answer: GoPubMed can also search the web. Go to
http://www.gopubmed.org/goweb and type addl antibody. Open chemicals
and drugs and click on antibodies, monoclonal. The search results are
reduced from 100 to 8. Besides many pages of the Alzforum, there is
the news that "Acumen and Merck Enter Into Alzheimer's Collaboration"
which talks about: "... exclusive rights Acumen's ADDL technology
monoclonal antibodies ... million development approval milestones
first antibody product is commercialized. ... "


Question: What treatments does the web offer for Alzheimer?

Answer: Go to http://www.gopubmed.org/goweb and type alzheimer
treatment. Go to chemicals and drugs and click on vitamins. We have
reduced the result set from 100 to 2 and learn that "vitamin may also
be an ideal natural treatment for Alzheimer's disease too.




---------------------------------------------------------

SOME MORE QUESTIONS:

Question: Which techniques are frequently used to study zebrafish 
development?
Question: Which processes are osteoclasts involved in?
Question: What are common histone modifications?
Question: Which diseases are associated with wnt signalling?
Question: Who publishes most at the MPI-CBG?
Question: Which diseases are asociated with HIV?
Question: Which are leading centers and scientists for liver 
transplantation?
Question: Which anatomical structure is affected by the bacterium 
helicobacter pylori?
Question: Which biological process is the protein Rab5 involved in and 
where is located in the cell?
Question: In which organisms is toluene degradation studied?
Question: Which enzymes are inhibited by aspirin?
Question: Which enzymes are important for congenital muscular dystrophy?


ANSWERS:

Question: Which techniques are frequently used to study zebrafish 
development?

Answer: Search for "zebrafish development". Under "top five and more" open
"techniques and equipment". In situ hybridization is listed
first. Clicking the term retrieves relevant articles.


Question: Which process are osteoclasts involved in?

Answer: Search for "osteoclast". Under "top five and more" open "biological
process". The first entry is "bone resorption".


Question: What are common histone modifications?

Answer: Search for "histone modification". Under "top five and more" 
open "biological sciences" and find methylation and acetylation.


Question: Which diseases are associated with wnt signalling?

Answer: Search for "wnt signalling". Under "top five and more" open 
"disease" and find "carcinoma" and many other cancer terms.


Question: Who publishes most at the MPI-CBG?

Answer: Search for "dresden[ad] planck[ad] genetics[ad]" and click on "show
statistics for these 302 articles".  Shevchenko A comes out top with
42 articles. Looks like he/she is doing work for two...


Question: Which diseases are asociated with HIV?

Answer: Type "HIV" and wait for the tree on the left to appear. Go to 
"top five & more" and click on "disease". Among others hepatitis and 
tuberculosis are mentioned. Clicking on tuberculosis retrieves the 
relevant articles including statements such as "HIV and parasitic 
co-infections in tuberculosis patients".


Question: Which are leading centers and scientists for liver 
transplantation?

Answer: Type "liver transplantation" and click on statistics for term 
"liver transplantation" at the top of the results page. Among the top 
authors is "P Neuhaus" and among the cities is "Berlin". Prof. Peter 
Neuhaus works at the Charite Hospital in Berlin, Germany, is a leading 
specialist in the field.


Question: Which anatomical structure is affected by the bacterium 
helicobacter pylori?

Answer: Type "helicobacter pylori", go to "top five & more" and open 
"anatomy" Among other terms "gastric mucosa" is listed. Hovering the 
mouse over the term reveals an explanation, which mentions that gastric 
mucosa is the lining of the stomach.


Question: Which biological process is the protein Rab5 involved in and 
where is located in the cell?

Answer: Type "rab5" and wait for the tree on the left to appear. Go to 
"top five & more". Click on biological process shows "endcytosis" and 
clicking on "cellular component" shows "endosomes". Hovering over the 
terms displays brief explanations of what endocytosis and endosomes are.


Question: In which organisms is toluene degradation studied?

Answer: Type "toluene degradation" and wait for the tree on the left to 
appear.
Go to "top five & more" and open "organisms". The bacteria pseudomonas 
are listed first. A click retrieves the relevant articles


Question: Which enzymes are inhibited by aspirin?

Answer: Type "aspirin" and wait for the tree on the left to appear. Go 
to "hierarchy of content" and then "chemicals and drugs" and "enzymes 
and co-enzymes". From there always click the top child until you reach 
"cyclooxygenase 1" and "cyclooxygenase 2". Clicking reduces the articles 
to a few which mention that aspirin inhibits cyclooxygenases.


Question: Which enzymes are important for congenital muscular dystrophy?

Answer: Type "congenital muscular dystrophy" and wait for the tree on 
the left to appear. Go to "hierarchy of content" and then "chemicals and 
drugs", "enzymes and co-enzymes", "enzymes", "transferases". There are a 
number of articles with statements such as "glycosyltransferases has 
revealed a novel mechanism for congenital muscular dystrophy."



-- 
---
Michael Schroeder, Professor in Bioinformatics

Biotec/Dept. of Computing, TU Dresden
Tatzberg 47-51, 01307 Dresden, Germany

w: www.biotec.tu-dresden.de
t: +49 351 463 400 60
f: +49 351 463 400 61
e: ms@biotec.tu-dresden.de

Received on Tuesday, 3 July 2007 11:14:09 UTC