Reading List for Database

Friday, April 9, 2010

"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

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

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

Use the concept of BLOCK to represent an annotated set of values and COLORS applied to the blocks to represent different annotations
the system can annotate both single values and the associations between multiple values
Does NOT account for negations. Only Select, Project, Join, Union

Observations: For an annotation mechanism to be useful in practice

we should be able to query values and annotations alike (in isolations and in unison)

"Annotating scientific data:why it is important and why it is difficult", Rajendra Bose, peter Buneman, Denise Ecklund

Some existing annotation systems:

Swiss-Prot: annotation database produced by specialist curators
TrEMBL: automated annotations for proteins ( link )
IBMdeveloperWorks: an annotation is an XML document that is linked to a target data object

Problems and solutions:

"pointers" to entries in other databases are sometimes used in the fields to provide mappings between co-ordinate systems
it's easy to propagate the annotations through the operations of the relational algebra BUT inverting these rules is non-deterministic because the annotation in the output could have come from more than one place in the input
An extension of SQL can be developed to propagate the annotations. One problem is when one attribute from two different tables, with two different annotations in each table, is part of the WHERE clause but not from SELECT clause. In this case, should both annotations be sent ? The solution can be to allow user to control the flow of annotation by adding some further propagation instructions to the SQL query
For reasons of database security many annotations are stored externally. They require a coordinate system in order to specify how they are to be attached to the data
External annotations can be retrieve by given the tuple: (table_name, tuple_id, the attribute_name) -- this can be a stable coordinate system

Open problems:

Many existing annotation system provide only a limited ability to query over annotation values
One needs to know where the annotation is attached to the base data and perhaps why it is attached. How can this be captured in the database and expressed in the query ?
Understanding the movement of annotations in the manually curated databases