Kalpana Krishnaswami

September 19, 2017

DistilBio Terms App now available in Elsevier’s ScienceDirect

The DistilBio Terms application detects  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.

Clicking on the terms takes the user to the DistilBio site that displays all the connections available for the term. The results are derived from many publicly available data sources such as Uniprot, Drugbank, PharmGKB, OMIM, CTD, Chembl, Chemspider, IntAct, MINT and Gene Ontology and presented as a set of connections.

Let us look at a paper and see how this app works. On opening the full text of a paper, the DistilBio terms is displayed  list of the terms detected in the paper and categorized into pathway, genes, proteins, drugs, diseases, compounds and organisms. The terms are also highlighted as clickable links in the text of the article.

Clicking on any of the terms displays the connections available for the particular term. Clicking on Breast Cancer in the above example displays the results as below.

Clicking on the name (as shown in red) takes the user to the DistilBio site where the user can explore further.

A disclaimer is that the context of some of the results shown may differ from what is refered to in the article. The user will have to use their discretion while viewing the results.

To install the app, follow the instructions below:

  1. To get started you will need to have an account on Elsevier’s Science Direct.  If you already do, please login at ScienceDirect and move on to the next step. If you don’t have an account you can create an account for free at ScienceDirect (click on Register on the top right of the page).
  2. Now open the “DistilBio Terms” app page and click on “Add Application”.
  3. Open any article on Science Direct and you will see a widget titled “DistilBio Terms” appear on the right column of the page.
  4. After the widget has loaded, click on any terms on the widget to view all connections for that specific term in DistilBio.

This app is best viewed in Firefox 3.4+ or Chrome 10.1+.

We would love to get your feedback on the app and if you found it useful.

September 19, 2017

Metaome releases the “DistilBio Terms Bookmarklet”

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.

The DistilBio bookmarklet detects the terms using relevant life-science ontologies and synonyms. Clicking on the terms takes the user to the DistilBio site that displays all the connections available for the term. The results are derived from many publicly available data sources such as Uniprot, Drugbank, PharmGKB, OMIM, CTD, Chembl, Chemspider, IntAct, MINT and Gene Ontology and presented as a set of connections.

To see how the bookmarklet works, let us look at an article related to biology on the net. I found a paper in plosone.org and clicked on the DistilBio Terms button. This displays a panel on the right of the page with a list of  detected in the paper and categorized into pathway, genes, proteins, drugs, diseases, compounds and organisms. Clicking on any of the terms takes the user to the DistilBio site and displays all the connections available for the term.

Try it on your data too

This app can also be used by users to find terms in their data which are not webpages. All the user has to do is go to http://terms.distilbio.com/tools and click on the “Try it” button. The user can now copy & paste their data in the box and hit submit. All biomedical concepts are detected and displayed as clickable links to the DisitlBio data.

The terms are displayed as below

A disclaimer is that the context of some of the results shown may differ from what is referred to in the article. The user will have to use their discretion while viewing the results.

Installing the bookmarklet is very simple.

  1. Go to http://terms.distilbio.com/tools.
  2. Display your Bookmarks bar by hitting Shift+Ctrl+B
  3. Drag the “DistilBio Terms” button (displayed in the site) to your Bookmarks bar.
  4. When you are browsing the web, push the “DistilBio terms” button to highlight all recognized terms in the page.

This app is best viewed in Firefox 3.4+ or Chrome 10.1+

We would love to hear from you. Do leave your feedback & suggestions as comments in this blog or drop us an email at info@metaome.com

September 19, 2017

DistilBio – New features and Data

Over the past few weeks we have been cheap beats ukadding new features and data to enhance the user experience. Some of the new features are detailed below.

Features:

Instant display of results

The query interface has been revamped to display results instantaneously as the user starts typing a query. Earlier, as the user created a query, nodes were formed in the panel above the search box and the user had to hit “Search” to view results. In the new release, as the user starts typing a query, the various options are displayed in the auto-complete and the results are simultaneously displayed in the result interface below the search box. The results displayed below changes dynamically as the user continues typing. For example, as the user types “Aspirin”, results are displayed instantly. Results change as the user continues adding letters to the search term. Users can also view the query nodes by clicking on the arrow above the query box.

Facet modification

Earlier, the facets in the result browser were static and sometimes this presented a problem when there were multiple  facets and user had to scroll down the page to find relevant data. Now, the facets can be maximized, minimized and moved around to view only the data the user in interested in viewing.

Provenance

One of the first things a researcher asks when he/she finds a connection between 2 concepts is “what is the provenance for this connection?” In the latest release of DistilBio, users can click on the connecting link between 2 facets and view the source of the data (displayed to the top right of the page) and also the curated publications for the links. The curated publications are derived from the source databases from which the data has been integrated.

Numerical operators

Querying using numerical operators is another feature that has been enabled in DistilBio. Many a times users while working on small molecules/drugs/proteins need to find molecules of a particular molecular weight or logP value etc.  Users can now build queries in DistilBio using numerical operators like <, >, =. For example, if a user wants to find all compounds that target the protein cdk1 in human.

Query: cdk1_human ---> compound

The results show 3326 compounds targeting the protein cdk1_human. To narrow down the list, the user can now find compounds with a molecular weight of say < 300.

Query: cdk1_human ---> compound ---> molecular weight <300

This narrows down the list to about 494 compounds. Similarly the user can further narrow down the list using LogP, LogD, ALogP values etc.

Regular expressions

There are instances when the user will want to find a drug, protein etc but will not know the complete name of the molecule. DistilBio now allows the use of regular expressions to enable the user find the search term easily. For example, if a user wants to find all the “Gliptins” and is not sure of the names of the drugs, the query can now be built as follows:

Query: *gliptin

From the drop-down, select the type “Drug ending with” to indicate that the name of the drug ends with gliptin.

Results displayed below will show that there are 3 gliptins – Saxagliptin, Sitagliptin, Vildagliptin. All the links available for the drugs are also displayed in the facets.

Data

Updated Data

Data has been updated for most datasets to the latest version available. Swissprot has been updated to the Dec 2012 release version. For a complete list of databases integrated in DistilBio have a look at the beats.

Protein domains

Protein domain data from Interpro has been added in DistilBio. Users can now query for proteins and find domains present in the protein and also find all proteins that contain a particular domain.

Query: cdk1_human > proteindomain

Results show 3 domains for the protein. For instance, if a user wants to find all proteins that contain the domain “Protein kinase, catalytic domain”, the user can extend the query by selecting the domain and clicking on extend and add the concept “protein” to the query.

Query: Protein kinase, catalytic domain > protein

This displays all proteins that contain the protein domain “Protein kinase, catalytic domain”

Small molecule Activity and assay data

Data from ChEMBL database has been updated to include data on bio-activities and assay. Users can now query for small molecules and their associated activities and also find bio-assays in which these compounds and activities have been measured.

Query: Compound > activity > assay

New properties for data from DrugBank and Swiss-Prot

DistilBio now covers most of the data available in DrugBank and Swiss-Prot.

New properties that have been added to the drug data from DrugBank include

  • Absorption
  • Brand Mixtures
  • Food Interactions
  • LogP
  • Manfacturer
  • Molecular Formula
  • Pharmacodynamics
  • pKa
  • Volume Of Distribution
  • Water Solubility

New connections and properties have also been added to protein data from Swiss-Prot. Connections that have been added include protein sites and regions like active site, binding site, metal binding regions, motifs etc. Users can also query for catalytic activities, PTM, induction, biophysicochemical properties such as Km, Vmax. Cross-references to databases covered in Swiss-Prot have also been included. For a complete list of connections and properties have a look at the of DistilBio.

We would love to hear your inputs on the latest release of DistilBio. You could respond to this blog or write to us at distilbio@metaome.com.

September 18, 2017

5 Ways Tech Gadgets Have Improved Our Lives

Technology is the founding stone of any civilization. The overall progress of any society depends on the most on scientific progress. This becomes evident if one looks at human history, which is in one sense a chronological account of scientific transitions from the simple to the complex. And now, in the 21 century, the world is more technology-dependent than it ever was.

Our lives have become so tech dependent that it has started to change the basic structure of our society. The invention of the internet, and subsequently, social network, has affected the very meaning of a community.

We have developed societal roles laced with rules different from the previous ones, and the way of information dissemination has seen a huge upgrade. On the other hand, gadgets have made our lives easier and productive. The biggest implication of this is the saving in time and money, and subsequently, it makes possible the pursuit of goals previously unattempted.

Smart Manufacturing

Tech Gadgets have revolutionized manufacturing. For example, using a 3D printer one can make copies of an item without having to go through the conventional procedure. A 3D printer lets a user build complex structures in a fraction of the time required in the conventional method. This has made possible the manufacturing of items, from simple yet ingenious toothpaste squeezers to lifesaving prosthetic limbs to real life castles.

Perceiving the Possible

Tech gadgets have made possible for us to create digital simulations which can be used to impart experience to human beings. For example, Virtual Reality can be used to train Pilots and Disaster Management workers to work in extreme conditions. On the other hand, Augmented Reality has been used to mix the real world with the digital, from making it possible to teach Australians about beach safety to figuring out the right place for furniture in a room before buying it.

Ease of Communication and Access to Information

The invention of the internet coupled with the advancement of electronic devices resulted in a big leap forward in terms of communication. An information that took days to in the least to travel from one point of the globe to another can now not only be sent in an instant but the exchange of information can be done in real time. This has made possible features like video calling from anywhere in the world.

Life expectancy

The advancement of medical instruments has made possible for the doctors and researchers to learn more about the human body and accordingly render cure. The MRI machine is a good example of this.

Recording History

The advancement of computers and the invention of complimentary gadgets such as closed-circuit cameras, advanced surveillance systems, and advanced storage systems, we have succeeded in recording a huge part of the day to day human life that not only has practical applications in the smooth functioning of law and order, but will also be important for us a race in the future to come.

Conclusion

Technology is ever-evolving. What exists today shall evolve into more efficient entities, and if one is grateful for being alive in a time like this they can scarcely be blamed.