XTractor- Biomedical Data Alerts

XTractor knowledgebase crosses 300000+ facts

mcjack — Thu, 22 Oct 2009 13:06:50 +0000

XTractor is one of its kind biomedical literature knowledgebase which updates refined facts from PubMed every single day.

The XTractor Premium Knowledgebase now has more than 300000 facts with more coverage of manually annotated drug and disease related facts published in PubMed…

The product is currently being widely used by more than 2000 researchers across the globe.

http://www.xtractor.in/premium

For a 1-month FREE Trial access: http://www.xtractor.in/trial.do

For trial access contact: http://www.xtractor.in/trial.do

XTractor Premium – Semantic Search over manually indexed data

mcjack — Thu, 08 Oct 2009 06:19:44 +0000

Searching through the vast repositories of biomedical literature, has been a long standing problem. XTractor Premium comes with a highly advanced semantic search feature which enables you to mine the most relevant information in matter of seconds. In comparison to similar application which guarantee results – XTractor Premium is far more effective in addressing scientific problems. We have multiple ontologies integrated into our semantic search panel, so that your search time is reduced.

EG: You could ask questions like:
Which are the GPCR class I receptors that are involved in colon cancer
OR which of the anti asthmatic drugs are also used for treatment diabetes type 2.

The search retrieves you the most significant results- due to the fact that XTractor relies on manual annotation of data. Manual annotation enables us to reduce the false positive mapping and also enables the correct alias/synonym mapping to a large extent. So inturn better results and faster discovery.

Many biomedical search engines talk about searching through the entire Medline but results are highly erroneous as they do not handle cases such as isoform specificity of a proteins and also since they are limited to keyword based or single entity based searching it gives the end user a limited chance to view all the published findings. Many of these search engines just run their query on the top 100 or 200 abstracts for refining purposes- but XTractor Premium with its inbuilt semantic search indexes is able to quickly compute multiple relationships across entities and enables faster generation of scientific hypothesis from the evergrowing XTractor knowledgebase of more than 250000 facts.

To use Semantic search feature- get a free access at:

http://www.xtractor.in/trial.do

The XTractor Premium Knowledgebase Touches 200000 mark within 1 year of its launch.

mcjack — Tue, 28 Jul 2009 05:55:15 +0000

XTractor Premium – a platform for discovery, analysis and modelling of published biomedical facts.

The application also comes with -XTractor Premium Knowledgebase - The ONLY Knowledgebase that gets updated everyday with manually annotated relationships from the latest PUBMED publications.

The XTractor Premium Knowledgebase now has more than 200000 facts updated in just 1 year of its launch providing information on Disease mechanisms, Biomarkers, Drug effects and interactions, Clinical trials, Prognosis, Pathways, Knockouts, Mutations, RNAi studies, and much more…

http://www.xtractor.in/premium

For a 1-month FREE Trial access: http://www.xtractor.in/trial.do

XTractor Premium on Nature Methods

mcjack — Tue, 21 Jul 2009 09:39:08 +0000

With the growing number of manually annotated biomedical relationships updated from latest PUBMED publications, XTractor Premium now makes its appearance in Nature Methods – a science methodology journal publishing laboratory techniques and methods papers in the life sciences and areas of chemistry.

The article can be accessed at: http://www.nature.com/app_notes/nmeth/2009/090906/full/an7147.html#a1

Title: “XTractor Premium – a Knowledgebase of manually annotated biomedical relationships updated everyday from PubMed abstracts”

Author: Guru Rao
/Molecular Connections Pvt. Ltd. Bangalore IN/

The article initially addresses the main drawbacks of data mining – the organization of the quantum of published data in PUBMED, time and cost consumed in analysing these data. It brings out the utilities of the XTractor Premium, which can accurately process this vast repertoire of scientific information with a quick turn around time. It also features the advanced analytical tools that come in handy with the XTractor Premium Knowledgebase such as Semantic Search, Concept linking, Bibliographic Search and comprehensive downloadable reports for faster analysis of the biomedical data.

The case study “Tracking common gene polymorphisms across multiple Diseases using XTractor” presented in the article provides the ability of XTractor Premium to help us discover newer facts in published literature within a quick 15-20 mins analysis time.

http://www.xtractor.in/premium

For a 1-month FREE Trial access: http://www.xtractor.in/trial.do

XTractor Premium – Increasing coverage of proteins, diseases, drugs and processes

mcjack — Fri, 10 Jul 2009 09:21:22 +0000

With the growing number of relationships, XTractor Premium Knowledgebase now contains a more comprehensive list of proteins, diseases, drugs and processes allowing the analysis of published biomedical facts on a wider range than before. We estimated the number of each of these entities annotated till date and found that XTractor Premium Knowledgebase currently covers 44% of Swiss Prot Proteins, 50 % of MesH diseases, 62% of Drugs from Drugbank and 17% of biological Processes from Gene Ontology DBs within one year of content.

http://www.xtractor.in/premium

For a 1-month FREE Trial access: http://www.xtractor.in/trial.do

What do Lung Cancer, Ovarian Cancer, Breast Cancer and Colon Cancer have in common?

mcjack — Fri, 03 Jul 2009 06:59:16 +0000

Common Proteins:

ABCB1, AKT1, AKT2, AKT3, ALDH1A1, AURKA, BCL2, BIRC5, CASP1, CASP3, CASP7, CASP8, CASP9, CCL2, CCND1, CCNE1, CD274, CD40, CD40LG, CD82, CD8A, CDH1, CDKN1A, CDKN1B, CDKN2A, CEACAM5, CTNNB1, CXCR4, DAG1, EGF, EGFR, EPHA2, ERBB2, ESR1, ESR2, FN1, FRAP1, GSTM1, HDAC1, HIF1A, HSPA5, IFNG, IGF1, IGF1R, IL1B, IL2, IL8, ITGB1, JUN, KRAS, KRT20, LEFTY2, LEP, MAP2K1, MAPK1, MAPK10, MAPK11, MAPK14, MAPK3, MAPK8, MAPK9, MKI67, MMP1, MMP13, MMP14, MMP2, MMP9, MUC1, MYC, NFKB1, NFKB2, PIK3C3, PIK3CA, PIK3CG, PIK3R1, PIK3R2, PLAU, PLAUR, PTEN, PTGS2, PTK2, PTK2B, RB1, REL, RELA, RELB, SCGB2A2, SRC, STAT3, STK11, TERT, TGFB1, TGFB2, TGFB3, TNF, TNFRSF10B, TNFSF10, TP53, TYMS, VEGFA, VEGFB, VEGFC, VIM

Common Processes:

angiogenesis, anti-apoptosis, apoptosis, autophagy, cell adhesion, cell cycle, cell cycle arrest, cell death, cell differentiation, cell growth, cell migration, cell proliferation, DNA Methylation, drug resistance, epithelial to mesenchymal transition, gene expression, gene silencing, growth, lymphangiogenesis, metabolism, methylation, negative regulation of cell growth, negative regulation of cell proliferation, response to hypoxia, response to oxidative stress, RNA interference, signal transduction

Common Drugs:

Cetuximab, Cisplatin, Doxorubicin, Etoposide, Fluorouracil, Gefitinib, Paclitaxel

Common Diseases:

Carcinoma, Hepatocellular; Carcinoma, Lewis Lung; Carcinoma, Renal Cell; Colorectal Neoplasms; Esophageal Neoplasms; Glioblastoma; Head and Neck Neoplasms; Inflammation; Kidney Neoplasms; Leukemia; Liver Neoplasms; Melanoma; Neoplasm Metastasis; Neuroectodermal Tumors; Osteosarcoma; Pancreatic Neoplasms; Prostatic Neoplasms; Skin Neoplasms; Stomach Neoplasms; Thyroid Neoplasms; Uterine Cervical Neoplasms; Uterine Neoplasms

Try XTractor Premium Semantic Search to know more: www.xtractor.in/premium

Mail us at xtractorpremium@molecularconnections.com

The XTractor Premium Knowledgebase Touches 188009 mark and still growing.

mcjack — Fri, 03 Jul 2009 06:41:21 +0000

XTractor Premium – a platform for discovery, analysis and modelling of published biomedical facts.

The application also comes with -XTractor Premium Knowledgebase - The ONLY Knowledgebase that gets updated everyday with manually annotated relationships from the latest PUBMED publications.

The XTractor Premium Knowledgebase now has more than 188009 relationships providing information on Disease mechanisms, Biomarkers, Drug effects and interactions, Clinical trials, Prognosis, Pathways, Knockouts, Mutations, RNAi studies, and much more…

http://www.xtractor.in/premium

For a 1-month FREE Trial access: http://www.xtractor.in/trial.do

XTractor Premium for scientists to access data stored in PubMed says Knowledgespeak

mcjack — Tue, 19 May 2009 12:43:03 +0000

Life sciences informatics company Molecular Connections, India, has announced the availability of XTractor Premium, a knowledge management platform, for the biomedical research community. The product is projected to provide scientists with new and refined ways to access the latest scientific facts from PubMed. Pharmaceutical companies, researchers and scientists can use the platform to identify, verify and develop predictive relationships from PubMed Literature.

Leveraging the ability to transform data to knowledge and to assist experts is seen to be crucial to the success of research investigation today. XTractor Premium offers several enhancements over the beta version in managing large volume of published biomedical data to accelerate decision making.

The XTractor knowledgebase currently contains 150,000 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions and disease mechanisms. The knowledgebase is updated everyday with manually annotated relationships from the latest PUBMED publications. Other premium features include semantic search functionality; concept linking; bibliographic search; and the option to save and export data in user-friendly formats.

Original PR click here

The XTractor Premium Knowledgebase surpasses 150000 mark

mcjack — Tue, 19 May 2009 12:37:51 +0000

XTractor Premium – a platform for discovery, analysis and modelling of published biomedical facts. The application also comes with -XTractor Premium Knowledgebase – the only knowledgebase, which provides “manually” annotated facts from PubMed on a daily basis.
The XTractor Premium Knowledgebase now has more than 150000 relationships.

Increased Time and Cost of mining PubMed everyday

mcjack — Mon, 04 May 2009 10:49:27 +0000

www.xtractor.in/premium

Researchers are benefited to the maximal when accurate content from Biomedical Literature is delivered on a real time basis. We estimated the amount of time, effort & cost that is involved in mining PubMed for the relevant Biomedical facts every single day.

We performed a search on PubMed for Breast Neoplasm over different time spans:

We then estimated the time that is required by a normal human annotator to pick & categorize the relevant sentences from each of these abstracts and annotate the sentences for Protein, Diseases, Drugs or Biological Processes.

We found to annotate 30 days of data on breast neoplasm it would take at least 1man day (taking into account from our past estimates that it would at least take 10 min to annotate one abstract). So extrapolating the amount of time required to annotate data on a single Search “ Breast Neoplasm” for 3 months or 90 days happens to be 11 man-days of effort and considerable cost.

The same would imply if you were to read and analyze the facts yourself.

So in order to annotate 50000 abstracts (it would amount to 50000 abstracts x 10 mins) = 500000 mins or 1041 man-days or ~ 3 years to annotate 1 month of literature findings from PubMed.

Solution:

The major bottleneck with manual curation as demonstrated above involves considerable time and cost. So in XTractor we have reduced the time involved in the manual annotation effort- by significantly cutting down the process steps to boost our internal productivity and turnaround time. So that in almost real-time basis we are able to serve you with the latest manually annotated scientific facts every single day.

ROI:

At XTractor we do manual annotation of more than 700 abstracts everyday that too at < $1 per day.

XTractor delivers you the handpicked, manually annotated facts within 10 days from the date of publication from PubMed.

FREE Trial at http://www.xtractor.in/premium/trial.do

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