ORegAnno-NAR07

"ORegAnno: an open access community-driven resource for regulatory annotations"

• an open-source, open-access database and literaturecuration system for community-based annotation of experimentallyidentified DNA regulatory regions, transcription factor binding sites and regulatory variants
• based on open-source technology and is comprised of a MySQL database with a Java-based web application that indexes new annotations using the Lucene search engine (http://lucene.apache.org/) and provides programmatic access to the underlying data using Hibernate (http://www.hibernate.org/) and SOAP Web Services
• this service is made for curation of publications

VBIGenomeACS

"Genome Annotation and Comparison System", J.Zhao, T.Xue, B.Yang, K.Williams,A.R.Wattam,R.Will,B.Sharp,R.Kenyon,O.Crasta,B.W.Sobral

• Build with ToolBus/PathPort system which provide a generic Web Service framework to integrate backend data sources through a business logic layer
• Web Service and XML are the core technologies for an extensible, scalable and open standard based bioinformatics tool framework
• The system was designed to use a distributed architecture; consists of a central registration database and multiple satellite category databases
• Central registration database provides the URL of each different category of databases as well as an entry point for each segment accession identifier. All the category databases share the same database schema, allowing for the Web service to fetch a detailed annotation from any of the databases on-the-fly.
• Support for the annotation edition and version control was build into the database schema but the implementation of this feature is left as future work

GeneCruiser: Bioinformatics Applications Note, 2005

"GeneCruiser: a web service for the annotation of microarray data", T.Liefeld, M.Reich, J.Gould, P.Zhang, P.Tamayo, J.P.Mesirov

• web service and web application designed to annotate genomic data
• provides a SOAP web service interface allowing other applications to make use of its functionality
  

BioBuilder -annotations platform for proteins -BMC Bioinformatics 04

"BioBuilder as a database development and functional annotation platform for proteins", J.D.Navarro, N,Talreja, S.Peri, BM.Vrushabendra, BP.Rashmi,N.Padma, V.Surendranath, C.K.Jonnalagadda, PS.Kousthub, N.Deshpande, K.Shanker, A.Pandey

• BioBuilder is a tool developed using CORBA; build as a component on top of ZOPE, an open source web applications server written in Python
• Annotations are supervised. An approval must be granted in order for the annotation to go through
• Made to work especially for manually creating a protein database
• To import data from another database, the data should be in a XML format or a protein specific format
  

Web database query interface annotation based on user collaboration-WuhamUJ06

"Web database query interface annotation based on user collaboration", Lin Wei, Lin Can, Meng Xiaofeng; Wuahan University Journal of Natural Sciences, 2006

• short paper for a vision based query interface annotation method
• The GOAL of the system: to provide stimulant web service for programmatic usage of the web database
  
• the interface annotation work combines automatic annotations methods and user anticipation to achieve much higher accuracy
• the annotations refer to the "meaning" of the elements of a form
• An URL is submitted to an URL fetcher from an interface repository; It is then transformed into a form-based query interface and an automatic process adds annotations over the block elements of the form; the annotations are send back to the user for review
  
• No experiments provided; supposedly the system has 80% accuracy
  

CIDR07_bdbms-Eltabakh

"bdbms -A database management System for Biological Data", Mohamed Y.Eltabakh, Mourad Ouzzani, Walid G.Aref

• an extensible prototype database engine for supporting and processing biological databases
• provides framework that allows adding annotations/provenance at multiple granularities (i.e: table, tuple, column, and cell levels) archiving and restoring annotations, and querying the data based on the annotation/provenance values
• an extension to SQL is introduced, Annotation-SQL or A-SQL, to support the processing and querying of annotations and provenance informations
• integrates the non-traditional indexing techniques inside bdbms: (1) supporting the multidimensional datasets via multidimensional indexing techniques; (2) supporting compressed datasets via novel external-memory indexes that work over the compressed data without decompressing it
• use of Space-partitioning trees for indexing objects in a multi-dimensional space
  

sigmod05_DBNotes-Tan

"DBNotes: A Post-It System for Relational Databases based on Provenance" , Laura Chiticariu, Wang-Chiew Tan, Gautav Vijayvargiya

• This is a short presentation of the system, but more clear than the VLDB version