euGenes .. Fish .. Fly .. Human .. Mouse .. Mosquito .. Rat .. Weed .. Worm .. Yeast

euGenes: about feature tables

The main program generating feature tables is the perl script genomefeat.pl in /tools/data-perls/ , but see also parseflyxml.pl, parsewormgff.pl, parsegolden.pl for org-specific feature extractors.

This '# gnomap-version 1' will likely be changed/improved somewhat. What is here is a working format that is efficient to use with the map display program (java-based).

The fields now defined are:

Feature (col1): name of feature, usually GenBank/EMBL compatible but generally whatever the source data has (w/ some minor changes for consistancy among organisms). Never null.
gene (col2): a name or visible label (should be called 'symbol' instead). May be null.
map (col3): org. specific map position, cytologic or other. May be null.
range (col4): phys. map base range for chromosome. The syntax for this is GenBank/EMBL/DDBJ feature table location. Never null.
ID (col5): database id of feature here is MEOW:xxxxx for euGenes database ID. May be null.
db_xref (col6): general collections of database cross-refs. Minimal set here as other euGenes data stores these, accessible thru id. May be null.
notes (col7): other info., unstructured. Usually null.

Example format:

# fly/features-2L.tsv
# Features for fly from BDGP/Celera/FlyBase data [ 20-December-2000]
# gnomap-version 1
# Feature gene    map     range                         id                db_xref         
source  fly     Chr 2L  1..22082480     -
gene    Nhe1    -       complement(98968..101637)       MEOW:FBgn0026787  FlyBase:FBan0012178,GadFly:CT9263       -
gene    M(2)21AB -      102694..109351                  MEOW:FBgn0005278  FlyBase:FBan0002674,GadFly:CT31903,GadFly:CT31899,GadFly:CT31907,GadFly:CT31901,GadFly:CT31790  -
gene    CG13694 -       complement(110631..111036)      MEOW:FBgn0031219  FlyBase:FBan0013694,GadFly:CT33151      - 
gene    CG4822  -       complement(111997..115661)      MEOW:FBgn0031220  FlyBase:FBan0004822,GadFly:CT41972,GadFly:CT41960,GadFly:CT41970,GadFly:CT15205 -

Value '-' or empty field indicates null value.
Leading '#' indicate comment, with only '# gnomap-version' a special comment, though I parse the '# Features for fly from BDGP/Celera/FlyBase data [ 20-December-2000]' comment.
The special 'source' feature, always? the first non-comment, with gene/symbol = organism (e.g. fly/worm/man/weed/...), the map = chromosome, and range = chromosome base range.

Next format version:

The current gnomap format is similar to GFF but with, to me, more useful and efficient combination of fields for maps (among other things with GFF one must read a bunch of lines like exons, sort and paste together for a single mapped feature).

The general idea for this gnomap format is to capture all of a DDBJ/EMBL/GenBank feature table statement in one efficiently parseable line. A future format might require a 'merge' style tab-separated file where the first line is a set of field keys. These keys would be "Feature", "location", plus any set of qualifiers defined the same as D/E/G qualifier tagset of http://www.ncbi.nlm.nih.gov/collab/FT/index.html, but with some variation to suit the need for fixed columns. A qualifier field could be added/removed from table depending on need. The parser should recognize first non-comment as a list of field keys.

Alternately, the qualifiers could be catenated in a single field, with /key="value" ; /key2="value2" structure. Your comments are welcome.

Possible version 2a:

# fly/features-2L.tsv
# Features for fly from BDGP/Celera/FlyBase data [ 20-December-2000]
# gnomap-version 2a
Feature location      gene    map                       id               db_xref                     note   
source  1..22082480   fly     Chr 2L   -
gene    complement(98968..101637) Nhe1    -             MEOW:FBgn0026787  FlyBase:FBan0012178,GadFly:CT9263       -
gene    102694..109351   M(2)21AB -                     MEOW:FBgn0005278  FlyBase:FBan0002674,GadFly:CT31903,GadFly:CT31899,GadFly:CT31907,GadFly:CT31901,GadFly:CT31790  -
gene    complement(110631..111036)  CG13694 -           MEOW:FBgn0031219  FlyBase:FBan0013694,GadFly:CT33151      - 
gene    complement(111997..115661)  CG4822  -           MEOW:FBgn0031220  FlyBase:FBan0004822,GadFly:CT41972,GadFly:CT41960,GadFly:CT41970,GadFly:CT15205 -

Possible version 2b:

# fly/features-2L.tsv
# Features for fly from BDGP/Celera/FlyBase data [ 20-December-2000]
# gnomap-version 2b
Feature location            qualifiers                   
source  1..22082480         /organism=fly ; /chromosome=2L 
gene    complement(98968..101637)    /gene=Nhe1 ; /id=MEOW:FBgn0026787 ; /db_xref=FlyBase:FBan0012178,GadFly:CT9263   
gene    102694..109351     /gene=M(2)21AB ; /id=MEOW:FBgn0005278  ; /db_xref=FlyBase:FBan0002674,GadFly:CT31903,GadFly:CT31899,GadFly:CT31907,GadFly:CT31901,GadFly:CT31790  -

File sets:

Current feature-xxx.tsv tables consist of one chromosome / linkage-unit of data (there is no 'chromosome' field, see the 'source' feature). The -xxx part is the chromosome name. Each set of chromosome features and associated dna-xxx.raw or dna-xxx.fasta files are located in organism folder. dna-xxx.raw is just the string of nucleotides that the features index onto.

With each feature-xxx.tsv is an associated feature-xxx.tsv.idx and feature-xxx.tsv.ranges. The feature-xxx.tsv.ranges consists of lines of

 base-start | file-index 
OR 
 class-name | file-index | location

where file-index indexes the feature-xxx.tsv file. It is used for efficient reading of subranges of features by the map display program.

The idmap.tsv table is a list of

  ID | Chromosome | base-start..base-end

for all chromosomes. It can be used to look up location by ID.

The feature-xxx.tsv.idx and idmap.tsv.idx files are a byte-index into respective files of based on numeric ID (idvalue * 8). The value stored there is the record-offset, record-length (two 4 byte integers) in feature-xxx.tsv or idmap.tsv.

Don Gilbert --- March 2001

Send comments to us at eugenes@iubio.bio.indiana.edu
euGenes uses Argos: A Replicable Genome infOrmation System