Do you have a long list of terms and want to find all connections available for them? There are times when you have a list of terms and finding connections for each of them, co-relating and analyzing the data can be a huge task. You can now upload your list on DistilBio using the Upload terms feature. We are excited to introduce this new feature to make your searching experience easier on DistilBio. Continue reading
Metaome has released the DistilBio Terms bookmarklet which detects and lists biomedical concepts such as genes, proteins, drugs, compounds and pathway mentioned in a webpage. This is similar to the app released by Metaome for Elsevier’s ScienceDirect. Now the app can be used on any webpage. The user has to install the bookmarklet in their browser’s bookmark bar once and has to only push the button to highlight all recognized terms in a page. Continue reading
Over the past few weeks we have been adding new features and data to enhance the user experience. Some of the new features are detailed below. Continue reading
Posted in Announcements, DistilBio
Tagged DistilBio, drugbank, evidence, features, new release, numerical operators, protein domain, provenance, regex, regular expression, swissprot
The DistilBio Terms application detects and lists biomedical concepts such as genes, proteins, drugs, compounds and pathway mentioned in the article. Once the user has installed the app, it is visible when viewing ScienceDirect articles and detects the terms using relevant life-science ontologies and synonyms. Continue reading
The DistilBio team has been working at improving the “autosuggest” to make querying easier and to display more relevant options to the user. Based on user feedback new features have been added to the autosuggest some of which are listed below. Continue reading
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 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:
- Are there specific databases you would like us to add?
- Are there specific types of data you would like us to add? Fore.g. gene expression data, clinical data etc.?
- Are there specific analysis tools that you would like us to add e.g. Blast, Clustalw etc.?
- Would a chemistry structure search be useful?
- How could we make the UI better to enhance the user experience?
- Could you we enhance the tool so it would suit specific communities centered on a model organism, a target or a disease?
- Would the tool be useful to search across private data?
- Anything else you can think of?
Any inputs would be welcome. You can respond on this blog, or write to me at firstname.lastname@example.org
CEO and Founder
Metaome Science Informatics
A new feature enhancement in DistilBio is 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 a user to build complex queries by showing the connections/properties available for each type.
Do give us your feedback!
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)
Posted in DistilBio, Use case
Tagged aromatase, assay, breast cancer, cell line, Chebi, Chembl, chemical compound, chemspider, compound, CP19A, DistilBio, drug discovery, letrozole, patent, tissue
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
- 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)
Posted in DistilBio
Tagged BLAST, cell image, cell image library, DistilBio, features, filter results, list query, more results, PDB structure, Query, save, save search, SPARQL, updates
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.
Posted in DistilBio
Tagged breast cancer, cross-reference, ctd, data source, DistilBio, drug, drugbank, Entrez Gene, epirubicin, IntAct, MINT, pharmgkb, Uniprot