User:Vincent Rouilly/Distributed Annotation System (DAS) for DNA Part Registries: Difference between revisions
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==DNA Part DAS Server== | |||
* Server address: | |||
* Typical queries: | |||
** retrieve all parts | |||
** retrieve all supported annotation types | |||
** retrieve DNA from a given part | |||
** retrieve all annotation from a given part | |||
** retrieve subparts from a given part | |||
** retrieve superparts from a given part | |||
==Software architecture== | ==Software architecture== | ||
==Implementation Steps== | ==Implementation Steps== | ||
We summarise here the different steps undertaken during this project. | |||
===Run Dazzle on the Google App Engine (GAE)=== | ===Run Dazzle on the Google App Engine (GAE)=== | ||
* Dazzle is a Java application that usually runs on a Tomcat server. However, GAE support Java applications, and no tweaking is necessary to run Dazzle on GAE. | |||
* [http://www.biojava.org/wiki/Dazzle:deployment_google_app_engine Instructions@BioJava] | |||
===Implement a BioSQL subset on top of the Google datastore=== | ===Implement a BioSQL subset on top of the Google datastore=== | ||
* BioSQL is a popular relational database model to store DNA sequences and annotations. | |||
* BioPython, BioJava, and BioPerl projects provide easy connectivity to the schema. | |||
* Google datastore is not a relational database. BioSQL schema has to be reformated into a more object oriented data model. | |||
* Only a BioSQL subset was considered for this project. Below is listed the implemented BioSQL tables: | |||
** Ontology and Term | |||
** Biodatabase, Bioentry, Biosequence, Bioentry_Qualifier_Value, Seqfeature, Location | |||
===Implement Dazzle plugin supporting BioSQL/datastore queries=== | ===Implement Dazzle plugin supporting BioSQL/datastore queries=== | ||
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==Project resources== | ==Project resources== | ||
* DAS standard specifications | * [http://www.biodas.org/wiki/Main_Page DAS standard] and its current specifications ([http://www.biodas.org/documents/spec.html v.1.53]) | ||
* Dazzle DAS server | * [http://www.biojava.org/wiki/Dazzle Dazzle DAS server] | ||
* BioSQL schema | * [http://www.biosql.org/wiki/Main_Page BioSQL] schema | ||
* BioPython | * [http://biopython.org/wiki/Main_Page BioPython] and [http://biojava.org/wiki/Main_Page BioJava] | ||
* [http://code.google.com/appengine/ Google App Engine documentation] | |||
* Google App Engine documentation | * BioSQL on GAE from Brad Chapman, see [http://bcbio.wordpress.com/2009/03/15/biosql-on-google-app-engine/ his blog post]. | ||
Revision as of 03:16, 28 August 2009
Distributed Annotation System for DNA Part Registries
Vincent 05:55, 28 August 2009 (EDT): This is a work in progress. If you are interested to contribute, or if you want some more info, please feel free to contact me.
Overview
- ...
- ...
Objectives
- ...
- ...
DNA Part DAS Server
- Server address:
- Typical queries:
- retrieve all parts
- retrieve all supported annotation types
- retrieve DNA from a given part
- retrieve all annotation from a given part
- retrieve subparts from a given part
- retrieve superparts from a given part
Software architecture
Implementation Steps
We summarise here the different steps undertaken during this project.
Run Dazzle on the Google App Engine (GAE)
- Dazzle is a Java application that usually runs on a Tomcat server. However, GAE support Java applications, and no tweaking is necessary to run Dazzle on GAE.
- Instructions@BioJava
Implement a BioSQL subset on top of the Google datastore
- BioSQL is a popular relational database model to store DNA sequences and annotations.
- BioPython, BioJava, and BioPerl projects provide easy connectivity to the schema.
- Google datastore is not a relational database. BioSQL schema has to be reformated into a more object oriented data model.
- Only a BioSQL subset was considered for this project. Below is listed the implemented BioSQL tables:
- Ontology and Term
- Biodatabase, Bioentry, Biosequence, Bioentry_Qualifier_Value, Seqfeature, Location
Implement Dazzle plugin supporting BioSQL/datastore queries
Process and Upload data from MIT Part Registry to Google App Engine (GAE)
Project resources
- DAS standard and its current specifications (v.1.53)
- Dazzle DAS server
- BioSQL schema
- BioPython and BioJava
- Google App Engine documentation
- BioSQL on GAE from Brad Chapman, see his blog post.
