Simple Search
We will illustrate a simple search by searching for proteins that are targeted by the drug Aspirin.
- 1.Type Aspirin into the search box. Select Aspirin (Drug) from the Autosuggest drop-down menu.
- Important: Clicking Search at this point will retrieve all known relationships to Aspirin.
- 2.Type Protein into the search box and select Protein from the menu.
- 3.Now select Targets as the relationship you interested in.
- 4. Click Search. Aspirin’s protein targets will be presented in the Protein facet in the RESULTS tab.
NOTE 1: The search term could be concepts such as Genes, Proteins, Diseases, Drugs etc. or could even be specific names such as BRCA1, MAPK, Sitagliptin etc.
NOTE 2: DistilBio interprets the queries as a graph where the nodes are the search terms and the selected relationship is the edge. The query graph can be viewed in the QUERY tab.
Link to Result
Advanced Search
DistilBio allows the user to ask complex queries and discover new and interesting connections across the data. An advanced search can be done by typing the “concept” and further extending the query by adding associated connections/concepts to the query. The “concept” could be a drug, gene, protein, disease, compound or properties related to these. The available connections for a concept are displayed by the autosuggest feature.
Currently, the “instant” mode cannot be disabled. The user can view and modify the query nodes by clicking on the arrow above the query box.
Some of the complex queries that can be asked are:
- What are the common drug targets between Aspirin and Acetaminophen?
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Type “Aspirin” in the search box and select the <type> drug. Aspirin in displayed in the search box with a green background. In the result interface below, all the connections available for Aspirin are displayed. The query can be extended by typing “protein” and selecting <type> protein from the dropdown. In the result interface, only the proteins targeted by Aspirin are displayed. Now type “acetaminophen” and select <type> drug. This completes the query and the results for the common drug targets between Aspirin and Acetaminophen are displayed in the result interface.
Link to Result - What are the protein targets of the drug Sitagliptin and what are the proteins interacting with these targets?
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Type “Sitagliptin” in the search box and select <type> drug. Type “protein” and select <type> protein from the dropdown. Again type “protein” and select type protein. This displays the protein targets of the drug Sitagliptin and also the proteins interacting with the protein targets.
Link to Result - What are the compounds targeting the protein CP19A and the assays associated with the compound? Also find assays performed only in humans
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Type “CP19A” in the search box. There are 19 matches for CP19A. To select the protein in human type “CP19A_human” or select from the drop-down. Now type “compound” and select the <type> compound. Type “assay” and select assay from the drop-down list. To find assays performed only in human, now type “human” and select <organism> human. This displays the results instantly below.
Link to Result
Data
DistilBio covers the following databases currently, and we're working on adding more.
| Database | Connections/Content |
|---|---|
| Swissprot | Protein->GO-Molecular Function, Protein->GO-Biological Process, Protein->GO-Cellular Component, Protein->Organism, Protein->Gene, Protein->Sites, Protein->Regions, Protein->Pathway, Protein->Protein Interaction, Protein->Disease, Protein->Publication, Protein->Protein Properties |
| Drugbank | Drug->Protein, Drug->Drug Interactions, Drug->Patent, Drug->Publication, Protein->Publication, Drug->Drug Properties |
| OMIM | Disease->Publication, Disease->Disease Properties |
| PharmGKB | Drug->Disease, Drug->Publication, Disease->Publication |
| CTD | Drug->Disease, Drug->Publication, Disease->Publication, Cross-Refs |
| Entrez Gene | Gene->Gene, Gene->Disease, Gene->Organism, Gene->Publication, Gene->GO-Molecular Function, Gene->GO-Biological Process, Gene->GO-Cellular Component, Disease->Publication, Gene->Gene Properties, Cross-Refs |
| Chebi | Compound->Patent, Compound->Publication, Compound->Compound Properties |
| Chembl | Activity->Publication, Activity->Assay, Assay->Publication, Assay->Protein, Assay->Organism, Compound->Protein, Compound->Assay, Compound->Activity, Compound->CellLine, Compound->Organism, Compound->Publication, Compound->Tissue, Compound->Compound Properties |
| ChemSpider | Cross-Refs for Compounds and Drugs |
| BioGRID | Gene->Gene Interaction, Gene Interaction->Publication |
| IntAct | Protein->Protein Interaction, Protein Interaction->Publication |
| MINT | Protein->Protein Interaction, Protein Interaction->Publication |
| HomoMINT | Protein->Protein Interaction, Protein Interaction->Publication |
| VirusMINT | Protein->Protein Interaction, Protein Interaction->Publication |
| GO | GO-Molecular function, GO-Biological Process, GO-Cellular Component, Labels and Names |
| INOH | Protein Classification |
| MeSH | Mesh terms |
| NCBI Taxonomy | Organism Labels and Names |
| InterPro | Protein->Publication, Protein Domain->Publication, Protein->GO-Cellular Component, Protein Domain->GO-Biological Process, Protein->Protein Domain, Protein->GO-Molecular Function, Protein Domain->GO-Cellular Component, Protein->GO-Biological Process, Protein Domain->GO-Molecular Function |
| Pubmed | Publication Titles |
| Cell Image Library | Image->GO-Molecular function, Image->GO-Biological Process, Image->GO-Cellular Component, Image->Imaging Mode, Image->Organism, Image->Source Of Contrast, Image->Image Type, Image->Parameters Imaged, Image->Cell Type, Image->Publication, Cell Type->Image, Image->Visualization Method, Cross-Refs |
| Cosmic* | Cell Line->Publication, Cell Line->Tissue, Cell Line->Disease, Cell Line->Gene, Mutation->Publication, Mutation->Gene, Mutation->Cell Line |
| CGP* | Cell Line->Tissue, Cell Line->Disease, Cell Line->Gene, Cell Line->Publication, Mutation->Gene, Mutation->Cell Line, Mutation->Publication, Cross-Refs |
| NCI* | Protein->Disease, Protein->Drug, Gene->Drug, Gene->Publication, Gene->Disease, Disease->Publication, Protein->publication, Drug->Publication |
| NCI-DTP* | Screening Study->Cell Line, Compound->Cell Line, Drug->Cell Line, Drug->Screening Study, Compound->Screening Study, Disease->Publication, Drug->Publication, Drug->Disease, Cross-Refs |
| CCLE* | Drug->Screening Study, Gene->Mutation, Gene->Cell Line, Cell Line->Tissue, Cell Line->Disease, Cell Line->Mutation, Mutation->Tissue, Compound->Screening Study, Screening Study->Cell Line |
| ICGC* | Mutation -> Gene, Disease -> Gene, Disease -> Patient, Patient -> Specimen, Specimen -> Specimen Properties, Mutation -> Mutation Properties, Patient -> Patient Properties, Cross-Refs |
| Methdb* | Gene -> GenomicRegion, GenomicRegion -> Experiment, GenomicRegion -> MethylationPattern, GenomicRegion -> Tissue, GenomicRegion -> MethylationProfile, GenomicRegion -> MethylationContent, Experiment -> Experiment Properties, GenomicRegion > GenomicRegion Properties, MethylationContent -> MethylationContent Properties, MethylationPattern -> MethylationPattern Properties, MethylationProfile -> MethylationProfile Properties |
| String* | OrthologousGroup -> Protein, Protein -> Protein Orthologs |
* Newly added databases.
- Drug-Disease
- Drug-Protein
- Drug-Gene
- Drug-Drug
- Drug-Publication
- Drug-Patent
- AHFS code
- ATC code
- Biotransformation
- Brand name
- CAS number
- Category
- Clearance
- Description
- Disease indication
- Group
- Inchi
- Inchi key
- IUPAC
- Half life
- Mechanism of action
- Molecular weight
- Protein binding
- Route of elimination
- SMILES
- Absorption
- Affected Organism Name
- Brand Mixtures
- Food Interactions
- LogP
- Manfacturer
- Molecular Formula
- Pharmacodynamics
- pKa
- Volume Of Distribution
- Water Solubility
- Disease-Drug
- Disease-Protein
- Disease-Gene
- Disease-Publication
- Disease-Image
- Disease-Patient
- Animal model
- Biochemical features
- Clinical features
- Description
- Diagnosis
- Inheritance
- Pathogenesis
- Gene-Protein
- Gene-Disease
- Gene-Drug
- Gene-Pathway
- Gene-Organism
- Gene-Publication
- Gene-Gene
- Gene-GOTerms
- Gene-GenomicRegion
- Chromosomal location
- Description
- Map location
- Symbol
- Protein-Disease
- Protein-Drug
- Protein-Pathway
- Protein-Protein
- Protein-Publication
- Protein-GO
- Protein-Compound
- Protein-Assay
- Protein- Activity
- Protein-Gene
- Protein-ProteinDomain
- Protein-ActiveSite
- Protein-BindingSite
- Protein-Calcium Binding Region
- Protein-Coiled-Coil Region
- Protein-Compositional Bias Region
- Protein-DNA Binding Region
- Protein-Glycosylation Site
- Protein-Intramembrane Region
- Protein-Lipid Binding Region
- Protein-Metal Binding Site
- Protein-Motif
- Protein-Mutagenesis Site
- Protein-Nucleotide Binding Region
- Protein-Transmembrane Region
- Protein-Zinc Finger Region
- Protein-Protein(Orthologs)
- Sequence
- Sequence Length
- Sequence Mass
- Sequence Similarity
- Function
- Related Gene Name
- Related Pathway Description
- Related Polymorphism Description
- Related Disease Description
- Recommended FullName
- Alternative FullName
- Recommended ShortName
- Alternative ShortName
- Sequence Similarity
- Induction Description
- Developmental Stage Expression Description
- Subcellular Location Description
- PTM
- Tissue-Specificity Description
- Subunit Structure Description
- Domain Description
- Cofactor Description
- Disruption Phenotype Description
- Enzyme Regulation Description
- RNA-Editing Description
- Catalytic Activity
- KM
- pH-Dependence
- Vmax
- Temperature-Dependence
- Redox Potential
- Pharmaceutical Use
- Biotechnological Use
- Allergen Property
- Toxic Dose
- pH-Dependence
- Redox Potential
- RNA-Editing Description
- Temperature-Dependence
- Compound-Assay
- Compound-Patent
- Compound-Cell line
- Compound-Tissue
- Compound-Organism
- Compound-Activity
- Compound-Publication
- Acidic pKa
- ALogP
- Basic pKa
- Canonical SMILES
- Charge
- Chemical structure
- Cescription
- H-bond acceptor
- H-bond donor
- Inchi
- Inchi key
- IUPAC
- Log D
- Log P
- Mass
- Molecular formula
- Molecular species
- Molecular weight
- SMILES
- Standard Inchi
- Standard Inchi key
- Mutation-Gene
- Mutation-Tissue
- Mutation-Cell line
- Mutation-Publication
- Somatic Status
- GRCh genome Position
- NCBI genome Position
- CDS Mutation
- Codon Change
- Amino Acid Mutation
- Validation platform
- Sequence Coverage
- Validation status
- Read count
- Platform
- Tumour genotype
- Reference genome allele
- Consequence type
- Nucleotode change
- Type
- Cell Line-Tissue
- Cell Line-Disease
- Cell Line-Mutation
- Cell Line-Gene
- Cell Line-Publication
- Expression Array
- SNP Array
- Patient Age
- Patient Gender
- Institute Address
Examples
Sample queries to get you started. Click on the links to try them out!!
Frequently Asked Questions
Search
- 1. How do I get started?
-
You can start your search by simply typing a query in the search box. Your query could be a gene, protein, drug, compound or a Biological process. As you type, the autosuggest will make relevant suggestions regarding the query term. Results appear instantly as the query is made.
You can add more terms to the query and select connections between the terms.
Examples can be found here
- 2. How complex can my query be?
-
Queries can range from simple keywords such as “aspirin” or “colon cancer” or complex ones such as proteins associated with colon cancer and the drugs targeting these proteins. In this case, query would read as colon cancer > associated protein > is target of drug (Try it on DistilBio).
More examples can be found here
- 3. What does the graph above the search box represent?
-
The graph is a visual representation of your query with each node representing a search term and the connections between the search terms.
- 4. Why do the results change as I build my query?
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As you type in your query term, DistilBio instantly displays the results for the term along with the connections available for the term. Results change as you continue typing and the query changes. For example, if your search term is “Aspirin”, as you start typing DistilBio recognizes “Asp” as the name of a gene and displays results below. When you continue typing, results change to terms recognized by DistilBio.
- 5. Can I use the results to make a new query?
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Yes, you can select any of the results and extend your query by clicking on the extend query button that appears on the facet.
- 6. How do I clear a query?
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You can clear your query by clicking on the “clear” button in the search box.
- 7. Where can I find my recent searches?
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You can find your recent searches in the panel to the left of the page marked “Recent Searches”. The last 10 searches will be listed in the panel.
- 1. Can I have a brief overview of the results page?
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- The results are displayed in a faceted view with one facet per concept and the connecting link between the facets. Clicking on a facet displays the details in the right panel.
- Clicking on the connecting link loads the source of the data in the box to the right side named “Source”.
- Clicking on the connecting link also loads curated references from the source databases in the right panel.
- 2. How do I minimize/maximize the facets?
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Facets can be minimized/maximized by clicking on the “+” at the top of the facet as shown below.
- 3. How do I select items listed in a facet?
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To select an item in the facet click the check-box to the left of the item. To select all the items in a facet click on the check-box at the top left side of the facet.
- 4. What are the various ways of filtering the results?
-
There are 2 ways of filtering the results. The results can be selected and filtered to display only instances and their relationships that a user is interested in. For instance, if a query is created for Aspirin – Protein – Disease, generally multiple target proteins and associated diseases are shown. Selecting a particular disease (using the check boxes) narrows the results showing only proteins connected with the selected diseases.
You can also filter the results by the source. For instance, if you want to look at data/connections only from DrugBank, selecting DrugBank in the source box displays results from DrugBank.
- 5. I’d like to see the query graph in the results page. Where is it?
-
Clicking on the arrow above the search box will bring the query graph panel down.
- 6. Why can’t I find any data for my query?
-
DistilBio currently covers specific databases and the data that you are looking for may not be available in the data source. We are constantly adding new datasets. Please use the feedback form to let us know what you were looking for and also if you would like to add any databases. Thank you for taking the time to give us your feedback.
- 7. How do I see more results than the ones displayed in the facet?
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If more data is available for your query DistilBio displays “Get more results” at the top of the result page. In queries with a single search term, you can click on the “More” button for each facet to view more results for the particular facet.
- 8. How do I find evidence for a triple?
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You can find the evidence for a triple by clicking on the connecting link between two facets. This displays the publication evidences for the connection in the right panel. These are curated evidences for source databases.
- 9. What are the various connections available?
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Check all the connections here
- 10. Why don’t I see some of the results I found previously?
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New versions of source databases are released and DistilBio updates data on a regular basis. Newer versions may have changes in data leading to new connections or loss of some connections.
- 11. How are the publications shown in the Evidence Card relevant?
-
The publications in the tab “Evidence for Connection” are curated publications that discuss a possible link between the 2 concepts that the user has queried for. These publications have been derived from the source databases from which the data has been integrated. The source database for a connection is mentioned in the box to the right of the page. The papers have not been curated by DistilBio.
- 12. Can I view the structure of a protein?
-
You can view the structure of a protein by going to the “Structure” tab in the right panel and selecting the structure you would like to view. This opens a new window with the structure that you have selected.
- 1. What are the databases currently covered by DistilBio?
-
Check all the databases here
- 2. What are the relationships currently covered by DistilBio?
-
Check all the relationships here
- 3. How often do you update the data?
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Release dates of our source databases are varied and we try to keep our data as updated as possible.
- 4. Does DistilBio curate data?
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Currently, DistilBio only curates data for the drug - disease connection from DrugBank.
- 5. What does “DistilBio inferred” mean?
-
In the Drug – Disease connection, DistilBio infers data by connecting the drug to its target proteins and the proteins to the diseases associated with it. This forms the “DistilBio inferred” connection for Drug – Disease via the protein targets. Similar results are available for Pathway related genes. This is inferred via the proteins related to the pathway.
- 6. What does the connection "associated" mean?
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This is a "generic" connection and is used across several concepts. The "associated" connection type does not specify causality. "Associated" has been used to link concepts such as Gene-Disease, Gene-Pathway, Disease-Protein. For example, Gene BRCA2 is associated with diseases Breast cancer, prostate cancer, Ovarian cancer etc.
- 7. What does the connection "related" mean?
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This is a "generic" connection and is used across several concepts. In the Drug-Disease relationship, "Related" refers to diseases where the drug may play a role either as a treatment for the disease or in the etiology of the disease i.e., Drug X maybe the cause of Disease Y. In the Drug-Protein connection, "related" refers to proteins that could be targets of the drug or may be associated with the drug either in its metabolism or as carrier, transporter etc. For example, Drug Ximelagatran has diseases drug induced abnormalities, embolism, thrombosis as related diseases. Ximelagatran causes drug induced abnormalities whereas it is used in the treatment of thrombosis. Drug Omeprazole has 25 proteins related to it and includes targets ATP4A, ATP4B and Cytochrome P 450 enzymes (CYP1A1,CYP1A2,CYP2C9 etc) that play a role in metabolism of drug.
- 8. Where can I find the source of the data?
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Sources for the results are displayed at the left of the page in the box named “Source”. Selecting the protein/drug etc. displays the data sources such as DrugBank, Uniprot.
- 9. What if I find an error in the data?
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Please use the feedback form to let us the details of the error. Thank you for taking the time to inform us about the error.
- 10. Can I suggest a database to be included in DistilBio?
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Yes, absolutely! Send us an email at info@metaome.com