Index

A

access control lists restricting adding classification groups isolates locus, [1], [2], [3], [4], [5] MLST scheme schemes allele definition records allele designations count query status allele sequence identify allele sequences adding alleles list query retiring un-retiring allelic profiles isolates amino acid variants locus annotation status query API authentication access token accessing protected resources consumer key request token session token user authorization API resources add submission correspondence create new submission DELETE /db/{database}/submissions/{submission_id} DELETE /db/{database}/submissions/{submission_id}/files/{filename} delete submission record delete submission supporting file download alleles in FASTA format download allelic profiles in CSV (tab-delimited) format download contigs in FASTA format download submission supporting file GET / GET /db GET /db/{database} GET /db/{database}/classification_schemes GET /db/{database}/classification_schemes/{classification_scheme_id} GET /db/{database}/classification_schemes/{classification_scheme_id}/groups GET /db/{database}/classification_schemes/{classification_scheme_id}/groups/{group_id} GET /db/{database}/contigs/{contig_id} GET /db/{database}/curators GET /db/{database}/fields GET /db/{database}/fields/{field} GET /db/{database}/genomes GET /db/{database}/isolates GET /db/{database}/isolates/{isolate_id} GET /db/{database}/isolates/{isolate_id}/allele_designations GET /db/{database}/isolates/{isolate_id}/allele_designations/{locus} GET /db/{database}/isolates/{isolate_id}/allele_ids GET /db/{database}/isolates/{isolate_id}/contigs GET /db/{database}/isolates/{isolate_id}/contigs_fasta GET /db/{database}/isolates/{isolate_id}/history GET /db/{database}/isolates/{isolate_id}/schemes/{scheme_id}/allele_designations GET /db/{database}/isolates/{isolate_id}/schemes/{scheme_id}/allele_ids GET /db/{database}/loci GET /db/{database}/loci/{locus} GET /db/{database}/loci/{locus}/alleles GET /db/{database}/loci/{locus}/alleles/{allele_id} GET /db/{database}/loci/{locus}/alleles_fasta GET /db/{database}/projects GET /db/{database}/projects/{project_id} GET /db/{database}/projects/{project_id}/isolates GET /db/{database}/schemes GET /db/{database}/schemes/{scheme_id} GET /db/{database}/schemes/{scheme_id}/fields/{field} GET /db/{database}/schemes/{scheme_id}/loci GET /db/{database}/schemes/{scheme_id}/profiles GET /db/{database}/schemes/{scheme_id}/profiles/{profile_id} GET /db/{database}/schemes/{scheme_id}/profiles_csv GET /db/{database}/sequences GET /db/{database}/submissions GET /db/{database}/submissions/{submission_id} GET /db/{database}/submissions/{submission_id}/files GET /db/{database}/submissions/{submission_id}/files/{filename} GET /db/{database}/submissions/{submission_id}/messages GET /db/{database}/users/{user_id} get summary of defined sequences list allelic profiles defined for scheme list classification schemes list database resources list loci list schemes list site resources POST /db/{database}/isolates/search POST /db/{database}/loci/{locus}/sequence POST /db/{database}/schemes/{scheme_id}/designations POST /db/{database}/schemes/{scheme_id}/sequence POST /db/{database}/sequence POST /db/{database}/submissions POST /db/{database}/submissions/{submission_id}/files POST /db/{database}/submissions/{submission_id}/messages query allele sequence query allele sequence without specifying locus query scheme designations query scheme sequences retrieve allele identifiers retrieve classification scheme information and groups, [1] retrieve contig record retrieve full allele designation record retrieve full allele information retrieve information about scheme field retrieve isolate record retrieve isolate update history retrieve list of allele designations retrieve list of alleles defined for a locus retrieve list of contigs retrieve list of curators retrieve list of groups for a classification scheme retrieve list of isolate provenance field descriptions retrieve list of isolate records retrieve list of isolate records that have genome assemblies retrieve list of isolates belonging to a project retrieve list of projects retrieve list of scheme allele identifiers retrieve list of submissions retrieve list of supporting files uploaded for submission retrieve locus record retrieve project information retrieve scheme allele designation records retrieve scheme information retrieve scheme loci retrieve specific allelic profile record retrieve submission correspondence retrieve submission record retrieve user information retrieve values set for a provenance field search isolate database upload submission supporting file

assembly stats auto allele definer stop automated assignment scheme profiles autotagger stop

B

batch profile definitions query batch uploading contigs - multiple isolates BLAST BLAST caches refreshing bookmarks

breakdown provenance field sequence bin two-field browse isolates scheme profiles BURST

C

caching schemes classification groups adding client authorization RESTful interface client databases clustering core genome codon usage Locus Explorer

composite fields config-specific downloads configuration export configuration settings validation core genome clustering count allele designations sequence tags

D

defining exemplar alleles deleting isolates, [1] profiles

downloads config-specific

E

exemplar alleles defining export configuration

extended attributes locus provenance fields

F

filters

G

gene presence; Genome Comparator genome filtering in silico hybridization in silico PCR geographic coordinates

geographic point lookup values populating GrapeTree minimum-spanning trees groups scheme

H

hosts mapping

I

identify allele sequence sequence type in silico hybridization in silico PCR in silico PCR analysis isolate records isolate aliases isolate record options

isolates adding allelic profiles browse deleting, [1] query retiring un-retiring updating, [1] uploading contigs iTOL phylogenetic trees

K

kiosk mode

Kleborate

L

LINcode schemes linking remote contigs list query alleles loci modifying display locus adding, [1], [2], [3], [4], [5] adding; copying existing record amino acid variants extended attributes SNPs

Locus Explorer codon usage polymorphic sites translated sequences locus positions setting

M

main results table options mapping hosts Microreact spatio-temporaral trees minimum-spanning trees GrapeTree PhyloViz online

MLST MLST scheme adding mod_perl modifying display loci schemes

O

offline curation auto allele definer autotagger options isolate record main results table provenance fields query

P

partitioning sets passwords setting setting; first user performance caching schemes mod_perl permissions locus curation scheme curation phylogenetic trees iTOL PhyloViz online minimum-spanning trees plugins enabling polymorphic sites Locus Explorer

polymorphisms populating geographic point lookup values profile records profiles deleting retiring un-retiring updating projects provenance field breakdown provenance fields extended attributes options publications, [1]

Q

query allele designations batch profile definitions isolates options scheme profiles sequence tags ST definitions from allelic profiles

R

records allele definition isolate profile sequence bin sequence tag refreshing BLAST caches

RESTful interface client authorization retiring alleles isolates profiles rMLST species identification storing analysis results

S

scheme groups scheme profiles automated assignment browse query schemes adding caching modifying display sequence bin breakdown query records sequence similarity determining sequence tag records sequence tags count query

sequence type identify sets partitioning SNPs locus sparsely-populated fields spatio-temporaral trees Microreact species identification rMLST ST definitions from allelic profiles query stop auto allele definer autotagger storing analysis results rMLST

T

translated sequences Locus Explorer

two-field breakdown

U

un-retiring alleles isolates profiles unique combinations updates disabling updating isolates, [1] profiles

uploading contigs isolates user groups user projects user types users adding