Guidelines and Procedures for Establishing and Maintaining EPD Cross-References

Purpose of this document:

The purpose of this document is to make clear for each type of Cross-references:
  1. The type-specific format of the cross-reference.
  2. The biological meaning of the cross-reference.
  3. The conditions and rules for establishing and maintaining of a cross-reference.
  4. The strategies for identifying new targets.
  5. The procedures for storage, update, verification of existing cross-references.

DR EPD

1. Format: 2. Biological meaning:


3. Conditions and rules:


4. Target identification:
5. Storage, maintenance and verification:


DR EMBL

1. Format: 2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:


DR SWISS-PROT

1. Format: 2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:


DR TRANSFAC

1. Format: 2. Biological meaning:


3. Conditions and rules:


4. Target identification:


5. Storage, maintenance and verification:


DR FLYBASE

1. Format: 2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:

DR MIM

1. Format: 2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:

DR MGD

1. Format:


2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:

APPENDICES

A1 Representation of Positional Sequence Objects Convention:

1. The Milano convention

The Milano convention for defining the position of SEQUENCES relative to a transcription inititation SITE (or another physiological sites wich logically falls between adjacent bases) is ilustrated by the following example. TRANSFAC applies the EMBL feature table numbering system for indicating a SITE or SUBSEQUENCE within a SEQUENCE. (Note that this problem is slightly different from the problem of indicating the position of a SEQUENCE relative to a SITE.) The FP lines of EPD follow the EMBL convention by referring to the first base of the transcript as the transcription initiation site.

2. Format for sequence object positions