Overview
In order to support convenient
analysis of SIMO sequence data using standard bioinformatics web services
and software, results of all SIMO database queries are available as downloadable
text files in FASTA
file format. Definition lines containing SIMO sequence IDs and taxonomic
and ecological context information (e.g. sampling date, environmental
characteristics, study site) are automatically generated from the database
for each sequence record.
The syntax for creating
user-defined HTTP queries (i.e. URL API) is described below for advanced
users or projects wishing to mine or create links to the SIMO database.
For additional assistance forming custom SIMO queries or linking to the
SIMO database, please email the SIMO
Database Administrator.
Syntax
Base
URL: http://simo.marsci.uga.edu/public_db/fasta_file.asp?
Parameter
Syntax: (i.e. appended to base url)
param1=xxx¶m2=yyy¶m3=zzz...
Supported
Parameters and Defaults:
| Parameter |
Description |
Default* |
| datemin |
minimum (earliest) sampling date
(e.g. 1/1/2002) |
none (any) |
| datemax |
maximum (latest) sampling date
(e.g. 12/31/2002) |
none (any) |
| season |
sampling season (Spring, Summer,
Fall, Winter) |
none (any) |
| envir |
code for environment sampled,
e.g. P, S, W
(see
HTML list values) |
none (any) |
| microenv |
code for microenvironment sampled,
e.g. PLD, WSW
(see
HTML list values) |
none (any) |
| zone |
code for marsh zone sampled, e.g.
CB, SS, TS, NO
(see
HTML list values) |
none (any) |
| max |
maximum number of records to return |
none (all) |
| genbank |
GenBank accession (e.g. AF439410) |
none (any) |
| simo |
SIMO clone/isolate code (e.g.
SIMO-300) |
none (any) |
| nucleotides |
nucleotide motif (e.g. ATGGA or
ATG?A) |
none (any) |
| minbases |
minimum sequence length (e.g.
300) |
0 |
| sourcetype |
sequence source type (CL or IS
for clone, isolate) |
none (any) |
| site |
code for SIMO sampling site, e.g.
DC, DM, DS
(see
HTML list values) |
none (any) |
| groupid |
taxonomic group numeric id (see
HTML list values) |
none (any) |
| groupname |
taxonomic group name **
(i.e. Phylum - Class, e.g. Bacteroidetes - Flavobacteria) |
none (any) |
| phylum |
phylum name (e.g. Proteobacteria) |
none (any) |
| seqid |
SIMO sequence numeric id (e.g.
103) |
none (any) |
| rowsize |
maximum length of nucleotide data
rows in FASTA file |
60 |
| sortcol |
database column to sort by (see
HTML list values) |
SequenceID |
| order |
sort order (ASC, DESC for ascending,
descending) |
ASC |
| defline |
Fasta
file definition line option:
verbose = sequence id followed by full description
sequin = id followed by NCBI Sequin modifiers
id = id only
alias = clone alias only (for SIMO use) |
verbose |
* default restriction if parameter or value are omitted from the
query string
** spaces should be encoded using %20 to avoid URL parsing errors
Example Syntax:
http://simo.marsci.uga.edu/public_db/fasta_file.asp?season=Summer&envir=P&
groupname=Proteobacteria%20-%20Gammaproteobacteria&minbases=300
Syntax Notes:
- queries should be entered on 1 line (example wrapped for web display
purposes only)
- a plain text message is returned if no matching records are returned
or an error occurs
- some parameter options are mutually exclusive (e.g. envir=P and
microenv=WSW, specifying plant environment and surface water microenvironment)
and therefore will always return no records
The Sapelo Island Microbial Observatory is funded by the National Science Foundation