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Standardization of information input

To input the information into the database, experts in biology annotate publications on the relevant experimental data.

 

 

 

To provide the standardization of information in TRRD, the program TRRD-INPUT was developed [Ananko E.A. et al., 1998]. This program produces an entry corresponding to an individual gene in a flat file form. It enables both editing and creating of new entries. Individual lines of an entry are checked for their compliance with the vocabularies supported within the TRRD database. Totally, TRRD contains 22 vocabularies comprising about 10829 words: six vocabularies are stable, the rest are being expanded.

The contents of the controlled vocabularies used by the program TRRD-INPUT for the standartization of data input in the TRRD is shown in the table.

The vocabulary type

Line code from the TRRD flatfile for this type of data

Number of entries in each vocabulary for TRRD (Aug-2003)
Name of an annotator

CR

44

Species name

OS

117

Key words

KW

641

Molecular product used to estimate the expression level

RT

2

Cell cycle stage

RY

20

Developmental stage

RD, TE

476

Organ

RO, TG

618

Tissue

RU, TU

225

Cells name

RN, TC

1607

Gene expression level

RL

11

External signal or cell inductor name

RI, TD

1128

Duration of the signalís effect

RH

103

The effect produced by external signal

FF

4

Regulatory region

RG

9

Site Preferred Name

NP

440

Transcription factor AC (according to TRANSFAC)

NF

2275

Factor  names and synonymous

TF, TY

2739

Origin of the factor

TO

7

Alteration of transcription level caused by binding of the factor to the site

AT

2

Codes of an experiment

AG

82

Names of external databases

DR

17

Journal names

SO

262

At present the vocabularies describing organs, tissues, and cells where the genes described in TRRD are expressed were essentially developed. Now these vocabularies are united and organized hierarchically. The highest level of vocabulary structure corresponds to organs and parts of organs. Organs are constituted out of tissues, which in turn contain different types of cells.

This hierarchy may be used for modification of the queries (generalization or specification) and for realization of associated search in TRRD.

 

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