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