Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract DASMIweb is a web server for the dynamic retrieval, integration, annotation, and assessment of protein and domain interactions.

It is based on a distributed system and allows the user to integrate and qualitatively assess interaction data from multiple external resources.

DASMIweb is a part of the DASMI. In a nutshell, it allows the user to retrieve interaction data from many distributed resources, unify these data, and qualitatively asses them.

DASMI is short for Distributed Annotation System for Molecular Interactions, a new approach for sharing, integrating, and assessing molecular interaction data.

DASMI is based on the Distributed Annotation System (DAS), a client- server system that aims at replacing central data repositories with distributed data sources.

The general idea of DAS and thus DASMI is that data should be kept with their original providers instead of being unified into central data warehouses.

While having the benefit of being fast and allowing complex queries, centralized resources have the drawback of:

1) Being rather rigid, as new data sources can only be included by the central authority, and;

2) Demanding a lot of maintenance work, because once the data has been incorporated into the warehouse, it has to be assured that it stays always up-to-date.

In a decentralized system like DASMI, new data sources can easily be incorporated, simply be setting up a new server, and the data is always recent, as it is maintained by its original providers.

More info on DAS --

The Distributed Annotation System (DAS) (see G6G Abstract Number 20488) defines a communication protocol used to exchange annotations on genomic or protein sequences.

It is motivated by the idea that such annotations should Not be provided by single centralized databases, but should instead be spread over multiple sites.

Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients.

The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organizations and the normal issues of release cycles, Application Programming Interface (API) updates and data duplication are avoided.

DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up 'sequence annotation' information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers.

Molecular Interactions supported by DASMIweb --

Currently, DASMIweb supports protein-protein and domain-domain interactions. You define the interaction type through the type of your query and your selection of data sources.

That is, if you are interested in retrieving interactions for a certain gene or protein, you simply issue a query by one of its database identifiers (e. g. an identifier from UniProtKB, RefSeq, and Entrez Gene).

If you are interested in interactions for a particular protein domain, you query DASMIweb with a Pfam identifier (PF00001) or name (AAA).

Interaction datasets currently included in DASMIweb --

DASMIweb currently has access to thirty-seven (37) distributed data sources.

Eleven (11) of these provide interaction data that has been experimentally determined or curated from scientific literature, twenty- four (24) data sources contain computational predictions, and two (2) data sources can be used for scoring the quality of interactions.

Note: Contact the manufacturer's web-site for additional info and a complete detailed list of Interaction datasets.

Querying DASMIweb --

To make querying DASMIweb as easy as possible, there is only a single query field. You simply insert the identifier of your target protein/domain and click the 'Query' button.

There is No need to specify the 'identifier system' (see below...) of your query identifier, DASMIweb will do that part for you and automatically try to determine the type of your query.

Only if the 'query identifier' is ambiguous, will it then ask you to specify it further.

Currently you can query for Interactions using either:

1) Entrez Gene ID (e.g. 3064);

2) UniProt accession number (e.g. P42858);

3) UniProt ID (e.g. HD_HUMAN);

4) Pfam ID (e.g. PF02861);

5) GeneInfo ID (e.g. 30582895);

6) RefSeq ID (e.g. NP_002102.4); and

7) Ensembl ID (e.g. ENSG00000100296).

DASMIweb Identifier or Coordinate system --

An Identifier system defines the types of the interactors that are participating in interactions. As DASMIweb retrieves the interaction data form various sources, it is crucial that the data provided by each source is properly defined.

An identifier system (e.g. Entrez,Gene_ID) is described by the four (4) fields - authority, type, version, and organism.

Authority is the name of the institution that defines the identifiers of the interactor(s), for instance, Entrez, UniProt, or Pfam.

Type denotes the physical dimension of the interactors, such as "Protein Sequence", "Protein Structure", or "Gene_ID".

Version and organism are optional fields to further define the interactors.

Identifiers can be mapped between different identifier systems. For example, genes are the blueprints for proteins, thus an identifier in the "Entrez,Gene_ID" identifier system can be mapped to at least one identifier in the "UniProt, Protein Sequence" identifier system and vice versa.

DASMIweb result presentation --

Information on the query interactors, such as names, synonyms, or external database references, is provided in the 'Information Panel'.

Interaction results are presented to the user in a table within the central 'Interaction Panel': 'table columns' represent data sources that have been queried for interactions, rows contain interaction partners (single partners for 'binary interactions' and all partners for 'protein complexes'), and squares in the intersections of rows and columns indicate 'particular interactions'.

Different background colors for each data source in the table header highlight the corresponding interaction determination methods: green represents sources with data derived from 'experimental studies' or curation of the 'scientific literature', yellow represents 'computational predictions'.

In addition, the interactions can be sorted according to individual table columns or by their frequency of occurrence in all data sources.

For the sake of clarity, a 'tabbed display' only shows a user-definable number of interactions per page (initially set to 50); arrows allow for browsing through additional results.

Display options like sorting and tabbed browsing can be configured in the 'myDASMI Panel'.

The manufacturer's tabular representation supports a quick ‘visual assessment’ of the results, based on the assumption that interactions that are reported in several datasets are more likely to be accurate.

To further investigate particular interactions, the user can click on an 'interaction square' and request the display of a new table row with additional information on an interaction and the interaction partner(s).

The amount of detail given in the additional info is primarily defined by the data source providers that reports the respective interaction and Not by DASMIweb.

System Requirements



Manufacturer Web Site DASMIweb

Price Contact manufacturer.

G6G Abstract Number 20487

G6G Manufacturer Number 104110