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 signal’s 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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