1. Barcode sequences at GenBank
Scott Federhen
NCBI/NLM/NIH
4 Jun. 2005

2. Archiving and Distributing Core Barcode Data Elements
1. Barcode sequences versioned and archived in INSD.
2. Core specimen annotation associated with sequence entries.
3. Links to specimen data, literature and ancillary resources.
4. Archive underlying raw data. (traces & quality scores)
5. Bulk submission tool for barcode sequences.

3. Core specimen annotation
organism - species name
isolate - field isolation name
specimen-voucher - voucher identifier
country - locality information
lat-lon - GPS coordinates
collection-date - minimal data about collection event
collected-by
identified-by
forward-primer - PCR primer data (for reproducibility)
reverse-primer
forward-primer-name
reverse-primer-name
note - free-text note
other GenBank qualifiers - cell-type; cell-line; sex; dev-stage; host ...
db-xref - explicit links to outside database entry

4. BARCODE requirements valid species name
5’ region of mtCOI (until other loci are approved by CBoL)
at least 500 bp; <1% ambiguous bases; bi-directional reads
(structured) specimen voucher (e-voucher if appropriate)
locality information (/country or /lat_lon)
primers
traces

5. new NCBI initiatives museum/herbarium/collections database
structured vouchers: <inst-code> <coll-code> <spec-id>
explicit checklists: ITIS, Species2000, uBio, ZooRecord ...
PubMed/PubMed Central expansion to systematic literature

6. barcode [keyword]
cbol

8. -------------------------------------------------------------------
linkid: 0
query: AF [accn]
query: AF [accn]
query: AF [accn]
rule:
name: Image of voucher specimen for DNA Sample 27-6

16. barcode[keyword]
Formicidae[orgn]
Diptera[subtree] AND species[rank]
(Craniata[subtree] NOT Tetrapoda[subtree]) AND species[rank]
NOT unspecified[prop] NOT loprovfishbase[filter]

18. Barcode Submission Tool
Contact
Information
Authors &
Citations
Global
Elements
mt COI
[genetic code]
[primers]
Source Modifiers
Nucleotide FASTA
Protein FASTA
Quality Scores

19. Source Modifiers Table