DistilBio: Tell us what you think

It has been two months since we launched DistilBio, our semantic search engine for the life sciences. We have had quite a bit of traction: so a big Cheap Burberry Outlet UK thanks to all those that visited. To those haven’t been there yet, we would be thrilled if you checked it out.

As we add new features and data to DistilBio, we would like this process to be user driven. This means that we would like you to tell us what you want. Searches across public data will remain free.

Input that we are specifically looking for:

  1. Are there specific databases you would like us to add?
  2. Are there specific types of data you would like us to add? Fore.g. gene expression data, clinical data etc.?
  3. Are there specific analysis tools that you would like us to add e.g. Blast, Clustalw etc.?
  4. Would a chemistry structure search be useful?
  5. How could we make the UI better to enhance the user experience?
  6. Could you we enhance the tool so it would suit specific communities centered on a model organism, a target or a disease?
  7. Would the tool be useful to search across private data?
  8. Anything else you can think of?

Any inputs would be welcome. You can respond Burberry Dresses on this blog, or write to me at kalpana@metaome.com

Thanks,
Kalpana Krishnaswami,
CEO and Founder
Metaome Science Informatics

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Autosuggest ranking in DistilBio – New feature

A new feature enhancement in DistilBio is Cheap Burberry Outlet UK ranking of terms in the autosuggest drop-down according to their relevance. Previously, for instance, while querying for a drug, the autosuggest would suggest properties of drugs according to alphabetical order.

This has been enhanced in the new version to rank “connections” related to the query higher over “properties”. The suggestions are also ranked in terms of the number of connections available for the particular query. For instance, when you query for a drug, the autosuggest now prompts the connections <interacts with> and <targets> as terms 1 and 2. Similarly for a disease, highest numbers of connections are available for <reference> and <related>. This is for “reference publications” and “related drugs” for the disease. This feature should make querying easier for Burberry Shirts a user to build complex queries by showing the connections/properties available for each type.

Do give us your feedback!

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Compound searches and their bio-activities in DistilBio

In my previous posts, I had focused on queries for drugs, diseases and proteins using DistilBio. Apart from this, DistilBio also contains data on bioactive chemical compounds from databases like ChEMBL and ChEBI. Experimental data properties, assays, cell line information for a compound are displayed in a simple and easily searchable faceted view.

I chose the compound “Letrozole” as an example to illustrate this. Letrozole is an approved drug used as an adjuvant treatment for hormonally-responsive breast cancer. Make sure the type “compound” is selected.  (Watch Demo Video)

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What’s new in DistilBio?

The last few weeks have seen a lot of new features added in DistilBio. While looking at the queries run by users and based on user feedback, we realized that the following were areas for improvement

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  • Ability to filter, refine and analyse results
  • “Ease of use of DistilBio”
  • Missing results which were known and relevant
  • Queries yielding no results

Let’s look at the issues a little closely and the measures taken by the DistilBio team to handle this. (Watch demo video)

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Where does this piece of Data come from?

DistilBio integrates data sets from various sources like Entrez Gene, Uniprot, DrugBank, PharmGKB, CTD, CHEMBL, protein interaction databases like IntAct, MINT etc. Each connection is backed by a data source.

Let us look at an example to see how data sources can be viewed in DistilBio.

I ran a query for breast cancer, the drugs used in the treatment and the proteins targeted by these drugs.

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DistilBio featured in Semantic Web

This week DistilBio was featured in semanticweb.com. The article discusses how bench biologists can leverage the wealth of information available across various datasets using DistilBio.

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“How does a user say what are the drugs used for Alzheimer’s disease and do they have certain protein targets and are those protein targets implicated in other diseases?”

Check out the Sitagliptin example featured in the post to see how DistilBio can be used. You can also check out more use cases from earlier posts about drug molecular side effects, drug repurposing and comparison of drugs.

For more on Metaome and DistilBio, read the original post - Metaome Helps Bench Biologists Get More Value From Linked Data [Semantic Web]

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Aspirin – Old drug, new roles?

In my last post, I looked at the different mechanism of actions of 3 OTC drugs – Aspirin, Acetaminophen and Ibuprofen. Aspirin a drug discovered ~100 years ago and in use for more than 50 years is one of the most common OTC drugs used. Aspirin is reported to be an analgesic, anti-pyretic, anti-inflammatory and anti-platelet agent. Recently I read a few reports that discussed the role of Aspirin in the prevention of cancer (1,2,3,4). This was really intriguing, that such a widely used drug with so many uses could also play a role in prevention of cancer.

As shown in my last post, aspirin and targets the COX1 and COX2 proteins and inhibits the formation of prostaglandins. Aspirin is also known to target other proteins.

I looked up DistilBio to find the protein targets of Aspirin. Continue reading

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Different strokes – Common painkillers and their mechanisms

We find a lot of over-the-counter (OTC) painkillers like aspirin, acetaminophen, ibuprofen. All these drugs though relieve pain and control fever, act in different ways and have different properties.  I thought it would be interesting to look at how these drugs act and the differences between the drugs.

First, I ran a query for aspirin, acetaminophen and ibuprofen in Distilbio to look at what I could find. Aspirin and Ibuprofen are categorized as NSAIDs (Non-steroidal anti-inflammatory drug) whereas acetaminophen is not an NSAID. I also ran a query to check if there are any common targets between these drugs. Continue reading

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Breast cancer gene BRCA and Heart disease

Recently I came across very interesting papers that report for the first time that women with risk of breast and ovarian cancer may have a higher risk of developing heart disease.

Mutations in the genes BRCA1 and BRCA2 have been associated with risk of breast and ovarian cancer. But now new research published in Nature Communications and the Journal of Biological Chemistry has found a new role for BRCA1 and BRCA2 as a “gatekeeper” of cardiac function and survival. Continue reading

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Understanding Drug Databases

While searching for information on Lumiracoxib in a few drug databases, I came across some confusing results. Lumiracoxib, is a non-steroidal anti-inflammatory drug that acts specifically on COX2. This drug was withdrawn in 2007 in Australia and subsequently in Canada and New Zealand due to concerns that it may cause liver damage.

I wanted to dig deeper into this and see how data for the same drug is represented by different databases, specifically the “drug to disease” relationship.  This made me look at a couple of more drugs, Cerivastatin and Ximelagatran that have been withdrawn from the market. Continue reading

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