diff --git a/CITATION.cff b/CITATION.cff
index 011de7cd8..d6900c93c 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
title: BridgeDb
message: 'If you use this software, please cite it as below.'
type: software
-version: 3.0.29
-date-released: 2025-07-28
+version: 3.0.30
+date-released: 2026-01-05
authors:
- given-names: Manas
family-names: Awasthi
diff --git a/README.md b/README.md
index 097e9c277..285d67cfb 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ Using BridgeDb dependencies
The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to
[Maven Central](https://search.maven.org/artifact/org.bridgedb/bridgedb-bundle), which means you can use the BridgeDb JARs without needing to compile BridgeDb.
-Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.0.29`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.0.30`:
For [Maven](https://maven.apache.org/):
@@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/):
org.bridgedb
org.bridgedb.bio
- 3.0.29
+ 3.0.30
```
@@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/):
For [Gradle](https://gradle.org/):
```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.29'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.30'
```
For [Ivy](http://ant.apache.org/ivy/):
```xml
-
+
```
For [Buildr](https://buildr.apache.org/):
```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.0.29'
+'org.bridgedb:org.bridgedb.bio:jar:3.0.30'
```
@@ -135,7 +135,7 @@ To make the release, run the following commands. Mind you, this requires you
to have an approved Sonatype (http://oss.sonatype.org/) account with push rights:
```shell
-mvn versions:set -DnewVersion=3.0.29
+mvn versions:set -DnewVersion=3.0.30
mvn clean deploy
```
@@ -145,7 +145,7 @@ and everything.
To make a development (SNAPSHOT) release, use:
```shell
-mvn versions:set -DnewVersion=3.0.30-SNAPSHOT
+mvn versions:set -DnewVersion=3.0.31-SNAPSHOT
mvn clean deploy
```
diff --git a/examples/pom.xml b/examples/pom.xml
index 2e91bde41..24513c825 100644
--- a/examples/pom.xml
+++ b/examples/pom.xml
@@ -3,7 +3,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
4.0.0
org.bridgedb.examples
diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml
index 17282758a..62614610a 100644
--- a/org.bridgedb.bio/pom.xml
+++ b/org.bridgedb.bio/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
index 812feb62d..cebedf6f7 100644
--- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
+++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
@@ -85,7 +85,7 @@ NCI Pathway Interaction Database Pid http://pid.nci.nih.gov/ http://pid.nci.nih.
OMIM Om http://omim.org/ http://omim.org/entry/$id 603903 gene 0 urn:miriam:mim ^[*#+%^]?\d{6}$ OMIM P492 omim gene,disease
OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ gene
ORCID orcid https://orcid.org https://orcid.org/$id 0000-0002-5355-2576 other Homo sapiens 1 urn:miriam:orcid ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ ORCID P496 orcid other,author
-Orphanet On http://www.orpha.net/consor/ https://identifiers.org/orphanet:$id 85163 other Homo sapiens 1 urn:miriam:orphanet ^\d+$ Bio2RDF orphanet other
+Orphanet On http://www.orpha.net/consor/ https://identifiers.org/orphanet:$id 85163 other Homo sapiens 1 urn:miriam:orphanet ^\d+$ Bio2RDF orpha other
Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob Oryzabase oryzabase.gene gene
Other O gene 1 O Other other
Pathway Commons Pc http://www.pathwaycommons.org/pc/ http://www.pathwaycommons.org/pc/record2.do?id=$id 485991 pathway 1 urn:miriam:pathwaycommons ^\d+$ Pathway Commons pathwaycommons pathway
@@ -123,7 +123,8 @@ SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/s
SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein
SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite
Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology
-TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene
+TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/locus?accession=$id 2200950 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^\d+$ TAIR Locus tair.locus gene
+TAIR gene name Agn https://www.arabidopsis.org/ https://www.arabidopsis.org/locus?name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.name ^AT[1-5]G\d{5}$ TAIR gene name araport gene
TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene
TTD Drug Td http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug ttd.drug metabolite
TTD Target Tt http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target ttd.target protein
diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv
index 940d8117d..415b7df5d 100644
--- a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv
+++ b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv
@@ -1,54 +1,549 @@
genus species short name symbol ncbi
+Abies grandis Grand fir Abg 46611
+Acer pseudoplatanus Ap 4026
Acetobacterium woodii Aw 33952
+Acetobacter subgen. Acetobacter As 151157
+Acinetobacter baylyi Ab 202950
+Actinidia chinensis Acc 3625
+Actinidia deliciosa Ad 3627
+Actinidia eriantha Ae 165200
+Adiantum capillus-veneris Ac 13818
+Adonis aestivalis Ada 113211
+Adonis annua Aan 212759
+Aegilops tauschii Ata 37682
+Agapanthus africanus African lily Al 51501
+Albizia julibrissin Aj 3813
+Allium aflatunense Aaf 70752
+Allium altaicum Aal 48666
+Allium altyncolicum Ala 165602
+Allium ampeloprasum Aam 4681
+Allium ascalonicum Aas 1476995
+Allium cepa Ace 4679
+Allium chinense Ach 130426
+Allium fistulosum Af 35875
+Allium nutans Anu 138328
+Allium ochotense Ao 669879
+Allium sativum Asa 4682
+Allium schoenoprasum Asc 74900
+Allium tuberosum Atu 4683
+Allium ursinum Au 4684
+Allium victorialis Av 88845
+Aloe arborescens Aar 45385
+Aloe ferox Afe 117798
+Amaranthus cruentus Acr 117272
+Amaranthus hypochondriacus Ah 28502
+Amorpha fruticosa Afr 48131
+Anaerotignum propionicum Apr 28446
+Anchusa officinalis Ano 89630
+Anethum foeniculum Afo 2849586
+Anigozanthos preissii Anp 95948
+Anisodus acutangulus Aac 402998
Anopheles gambiae Mosquito Ag 7165
+Anthriscus sylvestris Asy 48027
+Antirrhinum majus Am 4151
+Aphelandra squarrosa Asq 103766
+Apium graveolens Agr 4045
+Aquifex aeolicus Aae 63363
+Aquilaria crassna Aqc 223751
+Aquilegia vulgaris Avu 3451
+Arabidopsis lyrata Aly 59689
Arabidopsis thaliana Arabidopsis At 3702
+Arachis hypogaea Ahy 3818
+Archaeoglobus fulgidus Afu 2234
+Artemisia annua Aa 35608
+Asclepias syriaca Ass 48545
+Asparagus officinalis Aof 4686
Aspergillus niger Black mold An 5061
+Aspergillus terricola Ate 36642
+Astragalus bisulcatus Abi 20406
+Atractylodes lancea Atl 41486
+Atropa belladonna Abe 33113
+Auxenochlorella pyrenoidosa Apy 3078
+Avena clauda Acl 83523
+Avena longiglumis Alo 4500
+Avena prostrata Avp 279683
+Avena sativa Avs 4498
+Avena strigosa Ast 38783
+Avena ventricosa Ave 146535
+Bacillus anthracis Ba 1392
Bacillus subtilis Bsubtilis Bs 1423
+Barnadesia spinosa Bsp 171760
+Batis maritima Bm 4436
+Berberis stolonifera Bst 33814
Beta vulgaris Sugar Beet Bv 3555
+Betula pubescens Bp 38787
+Bifidobacterium longum Bl 206672
+Bixa orellana Bor 66672
Bos taurus Cow Bt 9913
-Brassica napus Rapeseed Bn 3708
+Botryococcus braunii Bb 1202541
+Brassica juncea Bj 3707
+Brassica napus Rapeseed Bn 3708
+Brassica nigra Bni 3710
+Brassica oleracea Wild cabbage Bo 3712
+Brassica rapa Br 3711
+Bromus inermis Bi 15371
+Bruguiera gymnorhiza Bg 39984
Caenorhabditis elegans Celegans Ce 6239
+Camellia irrawadiensis Cir 153142
+Camellia ptilophylla Cpt 319931
+Camellia sinensis Cas 4442
+Camellia taliensis Cta 182317
+Camptotheca acuminata Cac 16922
+Canavalia ensiformis Cen 3823
+Canavalia lineata Cli 28957
Canis familiaris Dog Cf 9615
+Cannabis sativa Csa 3483
+Capsicum annuum Caa 4072
+Capsicum baccatum Cb 33114
+Capsicum chinense Cch 80379
+Capsicum frutescens Cfr 4073
+Carapichea ipecacuanha Cip 77880
+Carica papaya Cp 3649
+Carpobrotus acinaciformis Caa 1053334
+Carthamus tinctorius Cti 4222
+Carum carvi Cc 48032
+Catharanthus roseus Madagascar periwinkle Car 4058
+Caulobacter vibrioides Cv 155892
+Celosia cristata Ccr 124768
+Centaurium erythraea Cer 172057
+Cephalocereus senilis Cse 223054
+Cerastium arvense Cea 271558
+Ceratodon purpureus Cpu 3225
+Cereibacter sphaeroides Csp 1063
+Cestrum elegans Cel 103475
+Chelidonium majus Cm 71251
+Chlamydia trachomatis Ctr 759363
+Chlamydomonas reinhardtii Cr 3055
+Chrysanthemum × morifolium C× 41568
+Chrysosplenium americanum Cam 36749
+Cicer arietinum Chickpea Cia 3827
+Cichorium intybus Cin 13427
+Cinchona calisaya Cca 153742
+Cinchona macrocalyx Cma 273779
+Cinchona mutisii Cmu 273780
+Cinchona officinalis Co 273781
+Cinchona pitayensis Cpi 128294
+Cinchona pubescens Cpb 50278
+Cinnamomum tenuipile Cte 192326
Ciona intestinalis Sea Squirt Ci 7719
+Citrullus lanatus Cl 3654
+Citrus × aurantium Cxa 43166
+Citrus × clementina Cxc 85681
+Citrus hanaju Ch 481547
+Citrus japonica Cj 76966
+Citrus junos Cju 135197
+Citrus maxima Cim 37334
+Citrus × microcarpa Cmi 164113
+Citrus × paradisi Cxp 37656
+Citrus sinensis Sweet orange Cs 2711
+Citrus trifoliata Cit 37690
+Citrus unshiu Cun 55188
+Clarkia breweri Cbr 36903
+Cleretum bellidiforme Cbe 90527
+Clitoria ternatea Clt 43366
+Clostridium acetobutylicum Cla 1488
+Clostridium botulinum Cbo 1491
+Clostridium kluyveri Ck 1534
Clostridium thermocellum Cthe Ct 1515
-Caulobacter vibrioides Cv 155892
+Coffea abeokutae Cab 213304
+Coffea arabica Coffee Ca 13443
+Coffea canephora Coc 49390
+Coffea eugenioides Ceu 49369
+Coffea liberica Col 49373
+Coleus scutellarioides Csc 4142
+Consolida orientalis Cor 565971
+Coptis japonica Coj 3442
+Coptis teeta Cot 261448
+Corallococcus coralloides Cco 184914
+Coreopsis grandiflora Cg 13449
+Corydalis vaginans Cva 3044017
+Crambe hispanica Chi 70124
+Crepis palaestina Cpa 72611
+Crocus sativus Crs 82528
+Croton stellatopilosus Cst 431156
+Croton sublyratus Csu 107238
+Cryptomeria japonica Cja 3369
+Cucumis melo Muskmelon Cme 3656
+Cucumis sativus Cucumber Cu 3659
+Cucurbita maxima Cum 3661
+Cucurbita pepo Cpe 3663
+Curcuma longa Clo 136217
+Cyanidioschyzon merolae Cym 45157
+Cystobacter fuscus Cfu 43
+Cytophaga hutchinsonii Chu 985
+Dahlia pinnata Dpi 101596
Danio rerio Zebrafish Dr 7955
+Daphne odora Do 329675
Daphnia magna Da 35525
Daphnia pulex Dp 6669
Dasypus novemcinctus Armadillo Dn 9361
+Datura inoxia Di 4075
+Datura stramonium Dst 4076
+Daucus carota Dca 4039
+Davallia trichomanoides Dt 328206
+Delftia acidovorans Dac 80866
+Delphinium grandiflorum Dg 85439
+Derris elliptica De 56063
+Desmodium uncinatum Dun 225101
+Dianthus caryophyllus Dc 3570
+Dicranum scoparium Ds 3222
+Dictyostelium discoideum Dd 44689
+Digitalis lanata Dl 49450
+Digitalis purpurea Dpu 4164
+Diospyros kaki Dk 35925
+Dolichandra unguis-cati Du 73871
Drosophila melanogaster Fruitfly Dm 7227
Echinops telfairi Hedgehog Et 9371
+Enterococcus faecalis Ef 1351
+Equisetum arvense Ea 3258
Equus caballus Horse Qc 9796
+Erwinia amylovora Eam 552
+Erythroxylum coca Erc 289672
Escherichia coli Ecoli Ec 562
+Eschscholzia californica Eca 3467
+Eucalyptus piperita Ep 87677
+Euglena gracilis Eg 3039
+Euonymus alatus Eal 4307
+Euphorbia lagascae El 54672
+Eustoma grandiflorum Egr 52518
+Fagopyrum esculentum Fe 3617
+Fagopyrum tataricum Ft 62330
+Fagus crenata Fc 28929
+Felis catus Fca 9685
+Flaveria bidentis Fb 4224
+Flaveria chlorifolia Fch 4228
+Fluviicola taffensis Fta 191579
+Forsythia × intermedia F× 55183
+Forsythia koreana Fk 205692
+Fragaria × ananassa F× 3747
+Galanthus elwesii Ge 82232
+Galium mollugo Gmo 254777
Gallus gallus Chicken Gg 9031
-Glycine max Soybean Gm 3847
+Gardenia jasminoides Gj 114476
+Gemmata obscuriglobus Go 114
+Gentiana straminea Gs 50768
+Gentiana triflora Gt 55190
+Gerbera hybrid Ghy 18101
Gibberella zeae Fusarium graminearum Gz 5518
+Ginkgo biloba Gb 3311
+Glandularia × hybrida G× 76714
+Glebionis segetum Gse 118509
+Glycine max Soybean Gm 3847
+Glycyrrhiza echinata Gec 46348
+Glycyrrhiza glabra Liquorice Gl 49827
+Gossypium arboreum Ga 29729
+Gossypium barbadense Gba 3634
+Gossypium hirsutum Ghi 3635
+Guatteria blepharophylla Gbl 402568
+Guatteria friesiana Gf 402569
+Guatteria hispida Gh 402570
+Haematococcus lacustris Hl 44745
+Halobacterium salinarum Hsa 2242
+Haloferax volcanii Hvo 2246
+Helianthus annuus Ha 4232
+Helianthus tuberosus Ht 4233
+Helicobacter pylori Hp 210
+Hevea brasiliensis Hb 3981
Homo sapiens Human Hs 9606
+Hordeum lechleri Hle 38856
Hordeum vulgare Barley Hv 4513
+Hydrangea macrophylla Hm 23110
+Hyoscyamus albus Hal 310458
+Hyoscyamus muticus Hmu 35626
+Hyoscyamus niger Hn 4079
+Hypericum androsaemum Han 140968
+Hypericum calycinum Hc 55963
+Hypericum perforatum Hpe 65561
+Hyphomicrobium zavarzinii Hz 48292
+Ilex paraguariensis Yerba mate Ip 185542
+Impatiens balsamina Ib 63779
+Ipomoea batatas Iba 4120
+Ipomoea nil In 35883
+Ipomoea purpurea Ipu 4121
+Juglans regia Jr 51240
+Kandelia candel Kc 61147
+Klebsiella oxytoca Ko 571
+Klebsiella pneumoniae Kp 1284798
+Lacticaseibacillus casei Lc 1312920
+Lactococcus lactis Ll 1358
+Lactuca sativa Ls 4236
+Lamium galeobdolon Lg 53161
+Lathyrus odoratus Lo 3859
+Lathyrus oleraceus Garden Pea Ps 3888
+Lavandula angustifolia Laa 39329
+Lawsonia inermis Li 141191
+Lemna aequinoctialis Lae 89585
+Lemna minor Lm 4472
+Lens culinaris Lcu 3864
+Leucaena leucocephala Lle 3866
+Lilium longiflorum Llo 4690
+Limnanthes alba Lal 42439
+Limnanthes douglasii Ld 28973
+Limonium latifolium Lla 227291
+Linum flavum Lf 407263
+Linum nodiflorum Ln 407264
+Linum perenne Lp 35941
+Linum usitatissimum Lu 4006
+Lithospermum erythrorhizon Le 34254
+Lotus corniculatus Lco 47247
+Lotus japonicus Lj 34305
Loxodonta africana Elephant La 9785
+Lunaria annua Lan 153659
+Lupinus albus Lua 3870
+Lupinus luteus Yellow lupine Llu 3873
+Lupinus polyphyllus Lpo 3874
+Lygodium circinatum Lci 84615
Macaca mulatta Rhesus Monkey Ml 9544
+Magnolia grandiflora Mg 3406
+Magnolia obovata Mo 349509
+Malus domestica Apple Mad 3750
+Malus hupehensis Mh 106556
+Malus pumila Mp 283210
+Manihot esculenta Cassava Me 3983
+Matthiola incana Mi 3724
+Medicago sativa Alfalfa Ma 3879
+Megathyrsus maximus Mma 59788
+Melilotus albus Mal 47082
+Mentha aquatica Maq 190902
+Mentha × gracilis M× 241069
+Mentha × piperita M× 34256
+Mentha spicata Ms 29719
+Methanocaldococcus jannaschii Mj 2190
+Methanosarcina mazei Mem 1434114
+Methanosarcina thermophila Mt 2210
+Methanothermobacter marburgensis Mmb 145263
+Methyloceanibacter caenitepidi Mc 1384459
+Methylococcus capsulatus Mca 414
+Methylorubrum extorquens Mex 408
+Methylosphaera hansonii Mha 51353
+Micrococcus luteus Mlu 1270
+Mirabilis jalapa Mja 3538
+Momordica charantia Mch 3673
Monodelphis domestica Opossum Md 13616
+Musa acuminata Mac 4641
Mus musculus Mouse Mm 10090
+Mycobacterium avium Mav 1764
+Mycobacterium kansasii Mk 1768
Mycobacterium tuberculosis Mtuberculosis Mx 1773
+Mycolicibacterium fortuitum Mf 1766
+Mycolicibacterium phlei Mph 1771
+Mycoplasmoides pneumoniae Mpn 1263835
+Nannocystis exedens Ne 54
+Narcissus pseudonarcissus Nps 39639
+Nepenthes alata Na 4376
+Nepenthes gracilis Ng 150966
+Nepenthes mirabilis Nm 150983
+Nepenthes rafflesiana Nra 150990
+Nerine bowdenii Nb 59042
+Neurospora crassa Nc 5141
+Nicotiana attenuata Nat 49451
+Nicotiana benthamiana Nbe 4100
+Nicotiana glutinosa Ngl 35889
+Nicotiana plumbaginifolia Np 4092
+Nicotiana rustica Nr 4093
+Nicotiana sylvestris Ns 4096
+Nicotiana tabacum Tabacco Nt 4097
+Nitrosopumilus maritimus Nma 338192
+Nothapodytes nimmoniana Nn 159386
+Ocimum basilicum Basil Ob 39350
+Olea europaea Oe 4146
+Ophiorrhiza japonica Opj 367363
+Ophiorrhiza pumila Op 157934
Ornithorhynchus anatinus Platypus Oa 9258
Oryctolagus cuniculus Rabbit Oc 9986
Oryza sativa Japanese Rice Os 4530
Oryzias latipes Medaka Fish Ol 8090
Ovis aries sheep Ova 9940
+Oxybasis rubra Or 3560
+Panax ginseng Pgi 4054
+Panax notoginseng Pno 44586
+Panicum miliaceum Pm 4540
+Panicum virgatum Pvi 38727
+Pantoea agglomerans Pag 549
+Pantoea ananatis Paa 553
Pan troglodytes Chimp Pt 9598
+Papaver somniferum Opium poppy Pas 3469
+Passiflora edulis Ped 78168
+Paullinia cupana Guarana Pc 392747
+Pelargonium crispum Pcr 1417776
+Pericallis cruenta Pec 98709
+Perilla frutescens Beefsteak plant Pe 48386
+Persea americana Pa 3435
+Persicaria tinctoria Pti 96455
+Petiveria alliacea Pal 46142
+Petroselinum crispum Pcs 4043
+Petunia x hybrida Pxh 4102
+Phaseolus coccineus Pco 3886
+Phaseolus lunatus Plu 3884
+Phaseolus vulgaris Common bean Pv 3885
+Phlebodium aureum Pau 218620
+Phleum pratense Ppr 15957
+Phragmites australis Phu 29695
+Physaria fendleri Pfe 63442
+Physaria lindheimeri Pl 439687
+Physcomitrium patens Pha 3218
+Picea abies Norway spruce Pia 3329
+Picea glauca Pg 3330
+Pimpinella anisum Pan 271192
+Pinus banksiana Pb 3353
+Pinus contorta Pic 3339
+Pinus densiflora Pde 77912
+Pinus ponderosa Ppo 55062
+Pinus sabiniana Psa 268869
+Pinus strobus Pst 3348
+Pinus sylvestris Psy 3349
+Pinus taeda Loblolly pine Pit 3352
+Plantago major Pma 29818
Plasmodium falciparum Malaria parasite Pf 5833
-Prymnesium parvum Pp 97485
+Plectranthus barbatus Pba 41228
+Plumbago europaea Peu 114226
+Plumbago indica Pin 122308
+Podophyllum peltatum Ppe 35933
+Pogostemon cablin Pca 28511
+Polaribacter filamentus Pfi 53483
+Populus alba Poa 43335
+Populus deltoides Pod 3696
+Populus nigra Pni 3691
Populus trichocarpa Western Balsam Poplar Pi 3694
+Portulaca grandiflora Pog 3583
+Prunus dulcis Pd 3755
+Prunus mume Pmu 102107
+Prymnesium parvum Pp 97485
+Pseudomonas aeruginosa Pae 1009714
+Pseudomonas fluorescens Pfl 294
+Psilotum nudum Pn 3240
+Pteris vittata Ptv 13821
+Pueraria montana Pmo 132459
+Punica granatum Pgr 22663
+Pyrus pyrifolia Ppy 3767
+Quercus robur Qro 38942
+Quercus rubra Qr 3512
+Raphanus sativus Rsa 3726
Rattus norvegicus Rat Rn 10116
+Rheum palmatum Rp 137221
+Rheum tataricum Rt 205071
+Rhizophora apiculata Ra 106626
+Rhizophora mangle Rm 40031
+Rhizophora stylosa Rst 98588
+Rhodiola rosea Rr 203015
+Rhodiola sachalinensis Rs 265354
+Rhodobacter capsulatus Rca 1061
+Rhodotorula glutinis Rgl 5535
+Rhus typhina Rty 255348
+Ricinus communis Castor bean Ri 3988
+Robinia pseudoacacia Rps 35938
+Rosa chinensis Rc 74649
+Rosa hybrid Rhy 128735
Rosmarinus officinalis Rosemary Ro 39367
+Rubia tinctorum Rti 29802
+Rubus idaeus Rid 32247
+Rudbeckia hirta Rh 52299
+Ruta graveolens Rg 37565
Saccharomyces cerevisiae Yeast Sc 4932
+Saccharopolyspora spinosa Ssp 60894
+Saccharum officinarum Sof 4547
+Salmonella enterica Se 28901
+Salvia fruticosa Greek sage Sf 268906
+Salvia fruticosa Sfr 268906
+Salvia officinalis Sao 38868
+Salvia rosmarinus Sr 39367
+Salvia splendens Spl 180675
+Sanguinaria canadensis Sca 3472
+Santalum album Saa 35974
+Santalum austrocaledonicum Sau 293154
+Santalum spicatum Sas 453088
+Sarcina ventriculi Sv 1267
+Saussurea medusa Sme 137893
+Saxifraga stolonifera Sst 182070
+Schizonepeta tenuifolia Ste 2849020
+Schizosaccharomyces pombe Sp 4896
+Scutellaria baicalensis Sba 65409
+Scutellaria viscidula Svi 512023
+Secale cereale Sce 4550
+Selaginella lepidophylla Sle 59777
+Senecio vernalis Sve 93496
+Senecio vulgaris Svu 76276
+Serratia marcescens Sma 1401254
+Sesamum alatum Sal 300844
+Sesamum indicum Si 4182
+Sesamum radiatum Sra 300843
+Sesbania rostrata Sro 3895
+Setaria italica Sit 4555
+Silene dioica Sd 39879
+Silene latifolia Sla 37657
+Simmondsia chinensis Sch 3999
+Sinningia cardinalis Sic 189007
+Sinopodophyllum hexandrum She 93608
Skeletonema marinoi Sm 267567
+Solanum aculeatissimum Scl 267265
+Solanum habrochaites Sh 62890
Solanum lycopersicum Tomato Sl 4081
-Solanum tuberosum St 4113
+Solanum melongena Som 4111
+Solanum pennellii Spe 28526
+Solanum tuberosum Potato St 4113
+Solidago canadensis Soc 59297
+Sorbus aucuparia Soa 36599
Sorex araneus Shrew Sa 42254
Sorghum bicolor Sorghum Sb 4558
+Spinacia oleracea Spinach So 3562
+Spirodela polyrhiza Spo 29656
+Sporobolus alterniflorus Spa 29706
+Stellaria media Stm 13274
+Stigmatella aurantiaca Sta 41
+Streptococcus mutans Smu 1309
+Streptococcus pneumoniae Spn 1001746
+Streptomyces antibioticus San 1890
+Streptomyces griseus Sg 1911
+Strobilanthes cusia Scu 222567
Sus scrofa Pig Ss 9823
+Syntrophotalea acetylenica Sac 29542
+Syzygium aromaticum Sar 219868
+Tagetes erecta Te 13708
+Tagetes patula Tp 55843
+Tanacetum balsamita Tb 301877
+Tanacetum vulgare Tv 128002
+Taxus baccata Tba 25629
+Taxus brevifolia Tbr 46220
+Taxus chinensis Tch 29808
+Taxus cuspidata Tcu 99806
+Tellima grandiflora Tg 29775
+Tetradesmus obliquus To 3088
Tetraodon nigroviridis Pufferfish Tn 99883
+Thalassiosira pseudonana Tps 35128
+Thalictrum flavum Tf 150094
+Thalictrum tuberosum Tt 79802
+Theobroma cacao Cocoa Tc 3641
+Thermococcus kodakarensis Tk 311400
+Thermotoga maritima Tma 2336
+Thuja plicata Tpl 3316
+Trichosanthes kirilowii Tki 3677
+Trifolium pratense Tpr 57577
+Trifolium repens Tr 3899
+Triglochin maritima Tm 55501
+Triticum spelta Ts 58933
+Triticum urartu Tu 4572
+Ulva curvata Green algea Uc 135247
+Ulva intestinalis Ui 3116
+Ulva lactuca Ul 63410
+Urochloa panicoides Up 37563
+Vaccinium myrtillus Vm 180763
+Vanilla planifolia Vp 51239
+Vernicia fordii Vf 73154
+Vibrio cholerae Vc 1225783
+Vibrio furnissii Vfu 29494
+Vicia faba Vfa 3906
+Vicia sativa Vs 3908
+Vigna aconitifolia Va 3918
+Vigna angularis Van 3914
+Vigna radiata Vr 157791
+Vigna unguiculata Vu 3917
Vitis vinifera Wine Grape Vv 29760
+Wachendorfia thyrsiflora Wt 95970
+Xanthomonas arboricola Xa 56448
+Xanthomonas axonopodis Xax 53413
Xenopus tropicalis Xenopus Xt 8364
+Zea luxurians Zl 15945
Zea mays Maize Zm 4577
+Zingiber officinale Zo 94328
+Zingiber zerumbet Zz 311405
+Zymomonas mobilis Zmo 542
diff --git a/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java b/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java
index 96a3d2ffe..0aa17a8ae 100644
--- a/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java
+++ b/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java
@@ -38,77 +38,525 @@ public enum Organism {
Unspecified("Unspecified", "Uns", 0),
+ AcerPseudoplatanus("Acer pseudoplatanus","Ap",4026),
AcetobacteriumWoodii("Acetobacterium woodii", "Aw", 33952),
+ AcetobacterSubgenAcetobacter("Acetobacter subgen. Acetobacter","As",151157),
+ AcinetobacterBaylyi("Acinetobacter baylyi","Ab",202950),
+ ActinidiaChinensis("Actinidia chinensis","Acc",3625),
+ ActinidiaDeliciosa("Actinidia deliciosa","Ad",3627),
+ ActinidiaEriantha("Actinidia eriantha","Ae",165200),
+ AdiantumCapillusveneris("Adiantum capillus-veneris","Ac",13818),
+ AdonisAestivalis("Adonis aestivalis","Ada",113211),
+ AdonisAnnua("Adonis annua","Aan",212759),
+ AegilopsTauschii("Aegilops tauschii","Ata",37682),
+ AlbiziaJulibrissin("Albizia julibrissin","Aj",3813),
+ AlliumAflatunense("Allium aflatunense","Aaf",70752),
+ AlliumAltaicum("Allium altaicum","Aal",48666),
+ AlliumAltyncolicum("Allium altyncolicum","Ala",165602),
+ AlliumAmpeloprasum("Allium ampeloprasum","Aam",4681),
+ AlliumAscalonicum("Allium ascalonicum","Aas",1476995),
+ AlliumCepa("Allium cepa","Ace",4679),
+ AlliumChinense("Allium chinense","Ach",130426),
+ AlliumFistulosum("Allium fistulosum","Af",35875),
+ AlliumNutans("Allium nutans","Anu",138328),
+ AlliumOchotense("Allium ochotense","Ao",669879),
+ AlliumSativum("Allium sativum","Asa",4682),
+ AlliumSchoenoprasum("Allium schoenoprasum","Asc",74900),
+ AlliumTuberosum("Allium tuberosum","Atu",4683),
+ AlliumUrsinum("Allium ursinum","Au",4684),
+ AlliumVictorialis("Allium victorialis","Av",88845),
+ AloeArborescens("Aloe arborescens","Aar",45385),
+ AloeFerox("Aloe ferox","Afe",117798),
+ AmaranthusCruentus("Amaranthus cruentus","Acr",117272),
+ AmaranthusHypochondriacus("Amaranthus hypochondriacus","Ah",28502),
+ AmorphaFruticosa("Amorpha fruticosa","Afr",48131),
+ AnaerotignumPropionicum("Anaerotignum propionicum","Apr",28446),
+ AnchusaOfficinalis("Anchusa officinalis","Ano",89630),
+ AnethumFoeniculum("Anethum foeniculum","Afo",2849586),
+ AnigozanthosPreissii("Anigozanthos preissii","Anp",95948),
+ AnisodusAcutangulus("Anisodus acutangulus","Aac",402998),
AnophelesGambiae("Anopheles gambiae", "Ag", "Mosquito", 7165),
+ AnthriscusSylvestris("Anthriscus sylvestris","Asy",48027),
+ AntirrhinumMajus("Antirrhinum majus","Am",4151),
+ AphelandraSquarrosa("Aphelandra squarrosa","Asq",103766),
+ ApiumGraveolens("Apium graveolens","Agr",4045),
+ AquifexAeolicus("Aquifex aeolicus","Aae",63363),
+ AquilariaCrassna("Aquilaria crassna","Aqc",223751),
+ AquilegiaVulgaris("Aquilegia vulgaris","Avu",3451),
+ ArabidopsisLyrata("Arabidopsis lyrata","Aly",59689),
ArabidopsisThaliana("Arabidopsis thaliana", "At", 3702),
+ ArachisHypogaea("Arachis hypogaea","Ahy",3818),
+ ArchaeoglobusFulgidus("Archaeoglobus fulgidus","Afu",2234),
+ AsclepiasSyriaca("Asclepias syriaca","Ass",48545),
+ AsparagusOfficinalis("Asparagus officinalis","Aof",4686),
Aspergillusniger("Aspergillus niger", "An", "Black mold", 5061),
+ AspergillusTerricola("Aspergillus terricola","Ate",36642),
+ AstragalusBisulcatus("Astragalus bisulcatus","Abi",20406),
+ AtractylodesLancea("Atractylodes lancea","Atl",41486),
+ AtropaBelladonna("Atropa belladonna","Abe",33113),
+ AuxenochlorellaPyrenoidosa("Auxenochlorella pyrenoidosa","Apy",3078),
+ AvenaClauda("Avena clauda","Acl",83523),
+ AvenaLongiglumis("Avena longiglumis","Alo",4500),
+ AvenaProstrata("Avena prostrata","Avp",279683),
+ AvenaSativa("Avena sativa","Avs",4498),
+ AvenaStrigosa("Avena strigosa","Ast",38783),
+ AvenaVentricosa("Avena ventricosa","Ave",146535),
+ BacillusAnthracis("Bacillus anthracis","Ba",1392),
BacillusSubtilis("Bacillus subtilis", "Bs", 1423),
+ BarnadesiaSpinosa("Barnadesia spinosa","Bsp",171760),
+ BatisMaritima("Batis maritima","Bm",4436),
+ BerberisStolonifera("Berberis stolonifera","Bst",33814),
BetaVulgaris("Beta vulgaris", "Bv", "Sugar Beet", 3555),
+ BetulaPubescens("Betula pubescens","Bp",38787),
+ BifidobacteriumLongum("Bifidobacterium longum","Bl",206672),
+ BixaOrellana("Bixa orellana","Bor",66672),
+ BosTaurus("Bos taurus", "Bt", "Cow", 9913),
+ BotryococcusBraunii("Botryococcus braunii","Bb",1202541),
BrachypodiumDistachyon("Brachypodium distachyon", "Bd", 15368),
+ BrassicaJuncea("Brassica juncea","Bj",3707),
BrassicaNapus("Brassica napus", "Bn", 3708),
- BosTaurus("Bos taurus", "Bt", "Cow", 9913),
- CoffeaArabica("Coffea arabica", "Ca", "Coffee", 13443),
+ BrassicaNigra("Brassica nigra","Bni",3710),
+ BrassicaRapa("Brassica rapa","Br",3711),
+ BromusInermis("Bromus inermis","Bi",15371),
+ BruguieraGymnorhiza("Bruguiera gymnorhiza","Bg",39984),
CaenorhabditisElegans("Caenorhabditis elegans", "Ce", "Worm", 6239),
+ CamelliaIrrawadiensis("Camellia irrawadiensis","Cir",153142),
+ CamelliaPtilophylla("Camellia ptilophylla","Cpt",319931),
+ CamelliaTaliensis("Camellia taliensis","Cta",182317),
+ CamptothecaAcuminata("Camptotheca acuminata","Cac",16922),
+ CanavaliaEnsiformis("Canavalia ensiformis","Cen",3823),
+ CanavaliaLineata("Canavalia lineata","Cli",28957),
CanisFamiliaris("Canis familiaris", "Cf", "Dog", 9615),
+ CannabisSativa("Cannabis sativa","Csa",3483),
+ CapsicumBaccatum("Capsicum baccatum","Cb",33114),
+ CapsicumChinense("Capsicum chinense","Cch",80379),
+ CapsicumFrutescens("Capsicum frutescens","Cfr",4073),
+ CarapicheaIpecacuanha("Carapichea ipecacuanha","Cip",77880),
+ CaricaPapaya("Carica papaya","Cp",3649),
+ CarpobrotusAcinaciformis("Carpobrotus acinaciformis","Caa",1053334),
+ CarthamusTinctorius("Carthamus tinctorius","Cti",4222),
+ CarumCarvi("Carum carvi","Cc",48032),
+ Caulobactervibrioides("Caulobacter vibrioides", "Cv", 155892),
+ CelosiaCristata("Celosia cristata","Ccr",124768),
+ CentauriumErythraea("Centaurium erythraea","Cer",172057),
+ CephalocereusSenilis("Cephalocereus senilis","Cse",223054),
+ CerastiumArvense("Cerastium arvense","Cea",271558),
+ CeratodonPurpureus("Ceratodon purpureus","Cpu",3225),
+ CereibacterSphaeroides("Cereibacter sphaeroides","Csp",1063),
+ CestrumElegans("Cestrum elegans","Cel",103475),
+ ChelidoniumMajus("Chelidonium majus","Cm",71251),
+ ChlamydiaTrachomatis("Chlamydia trachomatis","Ctr",759363),
+ ChrysanthemumxMorifolium("Chrysanthemum x morifolium","Cxm",41568),
+ ChrysospleniumAmericanum("Chrysosplenium americanum","Cam",36749),
+ CichoriumIntybus("Cichorium intybus","Cin",13427),
+ CinchonaCalisaya("Cinchona calisaya","Cca",153742),
+ CinchonaMacrocalyx("Cinchona macrocalyx","Cma",273779),
+ CinchonaMutisii("Cinchona mutisii","Cmu",273780),
+ CinchonaOfficinalis("Cinchona officinalis","Co",273781),
+ CinchonaPitayensis("Cinchona pitayensis","Cpi",128294),
+ CinchonaPubescens("Cinchona pubescens","Cpb",50278),
+ CinnamomumTenuipile("Cinnamomum tenuipile","Cte",192326),
CionaIntestinalis("Ciona intestinalis", "Ci", "Sea Squirt", 7719),
+ CitrullusLanatus("Citrullus lanatus","Cl",3654),
+ CitrusxAurantium("Citrus × aurantium","Cxa",43166),
+ CitrusxClementina("Citrus × clementina","Cxc ",85681),
+ CitrusxMicrocarpa("Citrus × microcarpa","Cmi",164113),
+ CitrusxParadisi("Citrus × paradisi","Cxp",37656),
+ CitrusHanaju("Citrus hanaju","Ch",481547),
+ CitrusJaponica("Citrus japonica","Cj",76966),
+ CitrusJunos("Citrus junos","Cju",135197),
+ CitrusMaxima("Citrus maxima","Cim",37334),
CitrusSinensis("Citrus sinensis", "Cs", "Sweet orange", 2711),
+ CitrusTrifoliata("Citrus trifoliata","Cit",37690),
+ CitrusUnshiu("Citrus unshiu","Cun",55188),
+ ClarkiaBreweri("Clarkia breweri","Cbr",36903),
+ CleretumBellidiforme("Cleretum bellidiforme","Cbe",90527),
+ ClitoriaTernatea("Clitoria ternatea","Clt",43366),
+ ClostridiumAcetobutylicum("Clostridium acetobutylicum","Cla",1488),
+ ClostridiumBotulinum("Clostridium botulinum","Cbo",1491),
+ ClostridiumKluyveri("Clostridium kluyveri","Ck",1534),
Clostridiumthermocellum("Clostridium thermocellum", "Ct", "Cthe", 1515),
- Caulobactervibrioides("Caulobacter vibrioides", "Cv", 155892),
+ CoffeaAbeokutae("Coffea abeokutae","Cab",213304),
+ CoffeaArabica("Coffea arabica", "Ca", "Coffee", 13443),
+ CoffeaCanephora("Coffea canephora","Coc",49390),
+ CoffeaEugenioides("Coffea eugenioides","Ceu",49369),
+ CoffeaLiberica("Coffea liberica","Col",49373),
+ ColeusScutellarioides("Coleus scutellarioides","Csc",4142),
+ ConsolidaOrientalis("Consolida orientalis","Cor",565971),
+ CoptisJaponica("Coptis japonica","Coj",3442),
+ CoptisTeeta("Coptis teeta","Cot",261448),
+ CorallococcusCoralloides("Corallococcus coralloides","Cco",184914),
+ CoreopsisGrandiflora("Coreopsis grandiflora","Cg",13449),
+ CorydalisVaginans("Corydalis vaginans","Cva",3044017),
+ CrambeHispanica("Crambe hispanica","Chi",70124),
+ CrepisPalaestina("Crepis palaestina","Cpa",72611),
+ CrocusSativus("Crocus sativus","Crs",82528),
+ CrotonStellatopilosus("Croton stellatopilosus","Cst",431156),
+ CrotonSublyratus("Croton sublyratus","Csu",107238),
+ CryptomeriaJaponica("Cryptomeria japonica","Cja",3369),
+ CucurbitaMaxima("Cucurbita maxima","Cum",3661),
+ CucurbitaPepo("Cucurbita pepo","Cpe",3663),
+ CurcumaLonga("Curcuma longa","Clo",136217),
+ CyanidioschyzonMerolae("Cyanidioschyzon merolae","Cym",45157),
+ CystobacterFuscus("Cystobacter fuscus","Cfu",43),
+ CytophagaHutchinsonii("Cytophaga hutchinsonii","Chu",985),
+ DahliaPinnata("Dahlia pinnata","Dpi",101596),
DanioRerio("Danio rerio", "Dr", "Zebra fish", 7955),
+ DaphneOdora("Daphne odora","Do",329675),
DaphniaMagna("Daphnia magna", "Da", 35525),
DaphniaPulex("Daphnia pulex", "Dp", 6669),
DasypusNovemcinctus("Dasypus novemcinctus", "Dn", "Armadillo", 9361),
+ DaturaInoxia("Datura inoxia","Di",4075),
+ DaturaStramonium("Datura stramonium","Dst",4076),
+ DaucusCarota("Daucus carota","Dca",4039),
+ DavalliaTrichomanoides("Davallia trichomanoides","Dt",328206),
+ DelftiaAcidovorans("Delftia acidovorans","Dac",80866),
+ DelphiniumGrandiflorum("Delphinium grandiflorum","Dg",85439),
+ DerrisElliptica("Derris elliptica","De",56063),
+ DesmodiumUncinatum("Desmodium uncinatum","Dun",225101),
+ DianthusCaryophyllus("Dianthus caryophyllus","Dc",3570),
+ DicranumScoparium("Dicranum scoparium","Ds",3222),
+ DictyosteliumDiscoideum("Dictyostelium discoideum","Dd",44689),
+ DigitalisLanata("Digitalis lanata","Dl",49450),
+ DigitalisPurpurea("Digitalis purpurea","Dpu",4164),
+ DiospyrosKaki("Diospyros kaki","Dk",35925),
+ DolichandraUnguiscati("Dolichandra unguis-cati","Du",73871),
DrosophilaMelanogaster("Drosophila melanogaster", "Dm", "Fruit fly", 7227),
- EscherichiaColi("Escherichia coli", "Ec", 562),
EchinposTelfairi ("Echinops telfairi", "Et", "Hedgehog", 9371),
-
- //NB: two-letter code is Qc to disambiguate from E. coli
+ EnterococcusFaecalis("Enterococcus faecalis","Ef",1351),
+ EquisetumArvense("Equisetum arvense","Ea",3258),
EquusCaballus("Equus caballus", "Qc", "Horse", 9796),
-
+ ErwiniaAmylovora("Erwinia amylovora","Eam",552),
+ EscherichiaColi("Escherichia coli", "Ec", 562),
+ EschscholziaCalifornica("Eschscholzia californica","Eca",3467),
+ EucalyptusPiperita("Eucalyptus piperita","Ep",87677),
+ EuglenaGracilis("Euglena gracilis","Eg",3039),
+ EuonymusAlatus("Euonymus alatus","Eal",4307),
+ EuphorbiaLagascae("Euphorbia lagascae","El",54672),
+ EustomaGrandiflorum("Eustoma grandiflorum","Egr",52518),
+ FagopyrumEsculentum("Fagopyrum esculentum","Fe",3617),
+ FagopyrumTataricum("Fagopyrum tataricum","Ft",62330),
+ FagusCrenata("Fagus crenata","Fc",28929),
+ FelisCatus("Felis catus","Fca",9685),
+ FlaveriaBidentis("Flaveria bidentis","Fb",4224),
+ FlaveriaChlorifolia("Flaveria chlorifolia","Fch",4228),
+ FluviicolaTaffensis("Fluviicola taffensis","Fta",191579),
+ ForsythiaxIntermedia("Forsythia × intermedia","Fxi",55183),
+ ForsythiaKoreana("Forsythia koreana","Fk",205692),
+ FragariaxAnanassa("Fragaria × ananassa","Fxa",3747),
+ GalanthusElwesii("Galanthus elwesii","Ge",82232),
+ GaliumMollugo("Galium mollugo","Gmo",254777),
GallusGallus("Gallus gallus", "Gg", "Chicken", 9031),
+ GardeniaJasminoides("Gardenia jasminoides","Gj",114476),
+ GemmataObscuriglobus("Gemmata obscuriglobus","Go",114),
+ GentianaStraminea("Gentiana straminea","Gs",50768),
+ GentianaTriflora("Gentiana triflora","Gt",55190),
+ GerberaHybrid("Gerbera hybrid","Ghy",18101),
GibberellaZeae("Gibberella zeae", "Gz", "Fusarium graminearum", 5518),
+ GinkgoBiloba("Ginkgo biloba","Gb",3311),
+ GlandulariaxHybrida("Glandularia × hybrida","Gxh",76714),
+ GlebionisSegetum("Glebionis segetum","Gse",118509),
GlycineMax("Glycine max", "Gm", "Soybean", 3847),
+ GlycyrrhizaEchinata("Glycyrrhiza echinata","Gec",46348),
+ GossypiumArboreum("Gossypium arboreum","Ga",29729),
+ GossypiumBarbadense("Gossypium barbadense","Gba",3634),
+ GossypiumHirsutum("Gossypium hirsutum","Ghi",3635),
+ GuatteriaBlepharophylla("Guatteria blepharophylla","Gbl",402568),
+ GuatteriaFriesiana("Guatteria friesiana","Gf",402569),
+ GuatteriaHispida("Guatteria hispida","Gh",402570),
+ HaematococcusLacustris("Haematococcus lacustris","Hl",44745),
+ HalobacteriumSalinarum("Halobacterium salinarum","Hsa",2242),
+ HaloferaxVolcanii("Haloferax volcanii","Hvo",2246),
+ HelianthusAnnuus("Helianthus annuus","Ha",4232),
+ HelianthusTuberosus("Helianthus tuberosus","Ht",4233),
+ HelicobacterPylori("Helicobacter pylori","Hp",210),
+ HeveaBrasiliensis("Hevea brasiliensis","Hb",3981),
HomoSapiens("Homo sapiens", "Hs", "Human", 9606),
+ HordeumLechleri("Hordeum lechleri","Hle",38856),
HordeumVulgare("Hordeum vulgare", "Hv", "Barley", 4513),
+ HydrangeaMacrophylla("Hydrangea macrophylla","Hm",23110),
+ HyoscyamusAlbus("Hyoscyamus albus","Hal",310458),
+ HyoscyamusMuticus("Hyoscyamus muticus","Hmu",35626),
+ HyoscyamusNiger("Hyoscyamus niger","Hn",4079),
+ HypericumAndrosaemum("Hypericum androsaemum","Han",140968),
+ HypericumCalycinum("Hypericum calycinum","Hc",55963),
+ HypericumPerforatum("Hypericum perforatum","Hpe",65561),
+ HyphomicrobiumZavarzinii("Hyphomicrobium zavarzinii","Hz",48292),
IlexParaguariensis ("Ilex paraguariensis", "Ip", "Yerba mate", 185542),
+ ImpatiensBalsamina("Impatiens balsamina","Ib",63779),
+ IpomoeaBatatas("Ipomoea batatas","Iba",4120),
+ IpomoeaNil("Ipomoea nil","In",35883),
+ IpomoeaPurpurea("Ipomoea purpurea","Ipu",4121),
+ JuglansRegia("Juglans regia","Jr",51240),
+ KandeliaCandel("Kandelia candel","Kc",61147),
+ KlebsiellaOxytoca("Klebsiella oxytoca","Ko",571),
+ KlebsiellaPneumoniae("Klebsiella pneumoniae","Kp",1284798),
+ LacticaseibacillusCasei("Lacticaseibacillus casei","Lc",1312920),
+ LactococcusLactis("Lactococcus lactis","Ll",1358),
+ LactucaSativa("Lactuca sativa","Ls",4236),
+ LamiumGaleobdolon("Lamium galeobdolon","Lg",53161),
+ LathyrusOdoratus("Lathyrus odoratus","Lo",3859),
+ LavandulaAngustifolia("Lavandula angustifolia","Laa",39329),
+ LawsoniaInermis("Lawsonia inermis","Li",141191),
+ LemnaAequinoctialis("Lemna aequinoctialis","Lae",89585),
+ LemnaMinor("Lemna minor","Lm",4472),
+ LensCulinaris("Lens culinaris","Lcu",3864),
+ LeucaenaLeucocephala("Leucaena leucocephala","Lle",3866),
+ LiliumLongiflorum("Lilium longiflorum","Llo",4690),
+ LimnanthesAlba("Limnanthes alba","Lal",42439),
+ LimnanthesDouglasii("Limnanthes douglasii","Ld",28973),
+ LimoniumLatifolium("Limonium latifolium","Lla",227291),
+ LinumFlavum("Linum flavum","Lf",407263),
+ LinumNodiflorum("Linum nodiflorum","Ln",407264),
+ LinumPerenne("Linum perenne","Lp",35941),
+ LinumUsitatissimum("Linum usitatissimum","Lu",4006),
+ LithospermumErythrorhizon("Lithospermum erythrorhizon","Le",34254),
+ LotusCorniculatus("Lotus corniculatus","Lco",47247),
LoxodontaAfricana ("Loxodonta africana", "La", "Elephant", 9785),
+ LunariaAnnua("Lunaria annua","Lan",153659),
+ LupinusAlbus("Lupinus albus","Lua",3870),
+ LupinusPolyphyllus("Lupinus polyphyllus","Lpo",3874),
+ LygodiumCircinatum("Lygodium circinatum","Lci",84615),
MacacaMulatta ("Macaca mulatta", "Ml", "Rhesus Monkey", 9544),
+ MagnoliaGrandiflora("Magnolia grandiflora","Mg",3406),
+ MagnoliaObovata("Magnolia obovata","Mo",349509),
+ MalusHupehensis("Malus hupehensis","Mh",106556),
+ MalusPumila("Malus pumila","Mp",283210),
+ MatthiolaIncana("Matthiola incana","Mi",3724),
+ MegathyrsusMaximus("Megathyrsus maximus","Mma",59788),
+ MelilotusAlbus("Melilotus albus","Mal",47082),
+ MenthaxGracilis("Mentha × gracilis","Mxg",241069),
+ MenthaxPiperita("Mentha × piperita","Mxp",34256),
+ MenthaAquatica("Mentha aquatica","Maq",190902),
+ MenthaSpicata("Mentha spicata","Ms",29719),
+ MethanocaldococcusJannaschii("Methanocaldococcus jannaschii","Mj",2190),
+ MethanosarcinaMazei("Methanosarcina mazei","Mem",1434114),
+ MethanosarcinaThermophila("Methanosarcina thermophila","Mt",2210),
+ MethanothermobacterMarburgensis("Methanothermobacter marburgensis","Mmb",145263),
+ MethyloceanibacterCaenitepidi("Methyloceanibacter caenitepidi","Mc",1384459),
+ MethylococcusCapsulatus("Methylococcus capsulatus","Mca",414),
+ MethylorubrumExtorquens("Methylorubrum extorquens","Mex",408),
+ MethylosphaeraHansonii("Methylosphaera hansonii","Mha",51353),
+ MicrococcusLuteus("Micrococcus luteus","Mlu",1270),
+ MirabilisJalapa("Mirabilis jalapa","Mja",3538),
+ MomordicaCharantia("Momordica charantia","Mch",3673),
MonodelphisDomestica ("Monodelphis domestica", "Md", "Opossum", 13616),
+ MusaAcuminata("Musa acuminata","Mac",4641),
MusMusculus("Mus musculus", "Mm", "Mouse", 10090),
+ MycobacteriumAvium("Mycobacterium avium","Mav",1764),
+ MycobacteriumKansasii("Mycobacterium kansasii","Mk",1768),
MycobacteriumTuberculosis ("Mycobacterium tuberculosis", "Mx", "Tuberculosis", 1773),
+ MycolicibacteriumFortuitum("Mycolicibacterium fortuitum","Mf",1766),
+ MycolicibacteriumPhlei("Mycolicibacterium phlei","Mph",1771),
+ MycoplasmoidesPneumoniae("Mycoplasmoides pneumoniae","Mpn",1263835),
+ NannocystisExedens("Nannocystis exedens","Ne",54),
+ NarcissusPseudonarcissus("Narcissus pseudonarcissus","Nps",39639),
+ NepenthesAlata("Nepenthes alata","Na",4376),
+ NepenthesGracilis("Nepenthes gracilis","Ng",150966),
+ NepenthesMirabilis("Nepenthes mirabilis","Nm",150983),
+ NepenthesRafflesiana("Nepenthes rafflesiana","Nra",150990),
+ NerineBowdenii("Nerine bowdenii","Nb",59042),
+ NeurosporaCrassa("Neurospora crassa","Nc",5141),
+ NicotianaAttenuata("Nicotiana attenuata","Nat",49451),
+ NicotianaBenthamiana("Nicotiana benthamiana","Nbe",4100),
+ NicotianaGlutinosa("Nicotiana glutinosa","Ngl",35889),
+ NicotianaPlumbaginifolia("Nicotiana plumbaginifolia","Np",4092),
+ NicotianaRustica("Nicotiana rustica","Nr",4093),
+ NicotianaSylvestris("Nicotiana sylvestris","Ns",4096),
+ NitrosopumilusMaritimus("Nitrosopumilus maritimus","Nma",338192),
+ NothapodytesNimmoniana("Nothapodytes nimmoniana","Nn",159386),
+ OleaEuropaea("Olea europaea","Oe",4146),
+ OphiorrhizaJaponica("Ophiorrhiza japonica","Opj",367363),
+ OphiorrhizaPumila("Ophiorrhiza pumila","Op",157934),
OrnithorhynchusAnatinus ("Ornithorhynchus anatinus", "Oa", "Platypus", 9258),
OryctolagusCuniculus ("Oryctolagus cuniculus", "Oc", "Rabbit", 9986),
- OryzaSativa("Oryza sativa", "Os", "Rice", 4530),
- OryzaJaponica("Oryza japonica", "Oj", "Rice"),
- OryzaSativaJaponica("Oryza sativa Japonica Group", "Osj", "Rice", 39947),
OryzaIndica("Oryza indica", "Oi", "Indian Rice"),
+ OryzaJaponica("Oryza japonica", "Oj", "Rice"),
+ OryzaSativa("Oryza sativa", "Os", "Rice", 4530),
OryzaSativaIndica("Oryza sativa Indica Group", "Osi", "Indian Rice", 39946),
+ OryzaSativaJaponica("Oryza sativa Japonica Group", "Osj", "Rice", 39947),
OryziasLatipes ("Oryzias latipes", "Ol", "Medaka Fish", 8090),
OvisAries("Ovis aries", "Ova", "Sheep", 9940),
+ OxybasisRubra("Oxybasis rubra","Or",3560),
+ PanaxGinseng("Panax ginseng","Pgi",4054),
+ PanaxNotoginseng("Panax notoginseng","Pno",44586),
+ PanicumMiliaceum("Panicum miliaceum","Pm",4540),
+ PanicumVirgatum("Panicum virgatum","Pvi",38727),
+ PantoeaAgglomerans("Pantoea agglomerans","Pag",549),
+ PantoeaAnanatis("Pantoea ananatis","Paa",553),
PanTroglodytes("Pan troglodytes", "Pt", "Chimpanzee", 9598),
+ PassifloraEdulis("Passiflora edulis","Ped",78168),
PaulliniaCupana("Paullinia cupana", "Pc", "Guarana", 392747),
+ PelargoniumCrispum("Pelargonium crispum","Pcr",1417776),
+ PericallisCruenta("Pericallis cruenta","Pec",98709),
PerillaFrutescens("Perilla frutescens", "Pe", "Beefsteak plant", 48386),
+ PerseaAmericana("Persea americana","Pa",3435),
+ PersicariaTinctoria("Persicaria tinctoria","Pti",96455),
+ PetiveriaAlliacea("Petiveria alliacea","Pal",46142),
+ PetroselinumCrispum("Petroselinum crispum","Pcs",4043),
+ PhaseolusCoccineus("Phaseolus coccineus","Pco",3886),
+ PhaseolusLunatus("Phaseolus lunatus","Plu",3884),
+ PhlebodiumAureum("Phlebodium aureum","Pau",218620),
+ PhleumPratense("Phleum pratense","Ppr",15957),
+ PhragmitesAustralis("Phragmites australis","Phu",29695),
+ PhysariaFendleri("Physaria fendleri","Pfe",63442),
+ PhysariaLindheimeri("Physaria lindheimeri","Pl",439687),
+ PiceaGlauca("Picea glauca","Pg",3330),
+ PimpinellaAnisum("Pimpinella anisum","Pan",271192),
+ PinusBanksiana("Pinus banksiana","Pb",3353),
+ PinusContorta("Pinus contorta","Pic",3339),
+ PinusDensiflora("Pinus densiflora","Pde",77912),
+ PinusPonderosa("Pinus ponderosa","Ppo",55062),
+ PinusSabiniana("Pinus sabiniana","Psa",268869),
+ PinusStrobus("Pinus strobus","Pst",3348),
+ PinusSylvestris("Pinus sylvestris","Psy",3349),
+ PlantagoMajor("Plantago major","Pma",29818),
PlasmodiumFalciparum("Plasmodium falciparum", "Pf", "Malaria Parasite", 5833),
-
- //NB: two-letter code is Pi to disambiguate from Pan troglodytes
+ PlectranthusBarbatus("Plectranthus barbatus","Pba",41228),
+ PlumbagoEuropaea("Plumbago europaea","Peu",114226),
+ PlumbagoIndica("Plumbago indica","Pin",122308),
+ PodophyllumPeltatum("Podophyllum peltatum","Ppe",35933),
+ PogostemonCablin("Pogostemon cablin","Pca",28511),
+ PolaribacterFilamentus("Polaribacter filamentus","Pfi",53483),
+ PopulusAlba("Populus alba","Poa",43335),
+ PopulusDeltoides("Populus deltoides","Pod",3696),
+ PopulusNigra("Populus nigra","Pni",3691),
PopulusTrichocarpa("Populus trichocarpa", "Pi", "Western Balsam Poplar", 3694),
+ PortulacaGrandiflora("Portulaca grandiflora","Pog",3583),
+ PrunusDulcis("Prunus dulcis","Pd",3755),
+ PrunusMume("Prunus mume","Pmu",102107),
PrymnesiumParvum("Prymnesium parvum", "Pp", 97485),
-
+ PseudomonasAeruginosa("Pseudomonas aeruginosa","Pae",1009714),
+ PseudomonasFluorescens("Pseudomonas fluorescens","Pfl",294),
+ PsilotumNudum("Psilotum nudum","Pn",3240),
+ PterisVittata("Pteris vittata","Ptv",13821),
+ PuerariaMontana("Pueraria montana","Pmo",132459),
+ PunicaGranatum("Punica granatum","Pgr",22663),
+ PyrusPyrifolia("Pyrus pyrifolia","Ppy",3767),
+ QuercusRobur("Quercus robur","Qro",38942),
+ QuercusRubra("Quercus rubra","Qr",3512),
+ RaphanusSativus("Raphanus sativus","Rsa",3726),
RattusNorvegicus("Rattus norvegicus", "Rn", "Rat", 10116),
+ RheumPalmatum("Rheum palmatum","Rp",137221),
+ RheumTataricum("Rheum tataricum","Rt",205071),
+ RhizophoraApiculata("Rhizophora apiculata","Ra",106626),
+ RhizophoraMangle("Rhizophora mangle","Rm",40031),
+ RhizophoraStylosa("Rhizophora stylosa","Rst",98588),
+ RhodiolaRosea("Rhodiola rosea","Rr",203015),
+ RhodiolaSachalinensis("Rhodiola sachalinensis","Rs",265354),
+ RhodobacterCapsulatus("Rhodobacter capsulatus","Rca",1061),
+ RhodotorulaGlutinis("Rhodotorula glutinis","Rgl",5535),
+ RhusTyphina("Rhus typhina","Rty",255348),
+ RobiniaPseudoacacia("Robinia pseudoacacia","Rps",35938),
+ RosaChinensis("Rosa chinensis","Rc",74649),
+ RosaHybrid("Rosa hybrid","Rhy",128735),
+ RubiaTinctorum("Rubia tinctorum","Rti",29802),
+ RubusIdaeus("Rubus idaeus","Rid",32247),
+ RudbeckiaHirta("Rudbeckia hirta","Rh",52299),
+ RutaGraveolens("Ruta graveolens","Rg",37565),
SaccharomycesCerevisiae("Saccharomyces cerevisiae", "Sc", "Yeast", 4932),
+ SaccharopolysporaSpinosa("Saccharopolyspora spinosa","Ssp",60894),
+ SaccharumOfficinarum("Saccharum officinarum","Sof",4547),
+ SalmonellaEnterica("Salmonella enterica","Se",28901),
+ SalviaFruticosa("Salvia fruticosa", "Sf", "Greek sage", 268906),
+ SalviaOfficinalis("Salvia officinalis","Sao",38868),
+ SalviaRosmarinus("Salvia rosmarinus","Sr",39367),
+ SalviaSplendens("Salvia splendens","Spl",180675),
+ SanguinariaCanadensis("Sanguinaria canadensis","Sca",3472),
+ SantalumAlbum("Santalum album","Saa",35974),
+ SantalumAustrocaledonicum("Santalum austrocaledonicum","Sau",293154),
+ SantalumSpicatum("Santalum spicatum","Sas",453088),
+ SarcinaVentriculi("Sarcina ventriculi","Sv",1267),
+ SaussureaMedusa("Saussurea medusa","Sme",137893),
+ SaxifragaStolonifera("Saxifraga stolonifera","Sst",182070),
+ SchizonepetaTenuifolia("Schizonepeta tenuifolia","Ste",2849020),
+ SchizosaccharomycesPombe("Schizosaccharomyces pombe","Sp",4896),
+ ScutellariaBaicalensis("Scutellaria baicalensis","Sba",65409),
+ ScutellariaViscidula("Scutellaria viscidula","Svi",512023),
+ SecaleCereale("Secale cereale","Sce",4550),
+ SelaginellaLepidophylla("Selaginella lepidophylla","Sle",59777),
+ SenecioVernalis("Senecio vernalis","Sve",93496),
+ SenecioVulgaris("Senecio vulgaris","Svu",76276),
+ SerratiaMarcescens("Serratia marcescens","Sma",1401254),
+ SesamumAlatum("Sesamum alatum","Sal",300844),
+ SesamumIndicum("Sesamum indicum","Si",4182),
+ SesamumRadiatum("Sesamum radiatum","Sra",300843),
+ SesbaniaRostrata("Sesbania rostrata","Sro",3895),
+ SetariaItalica("Setaria italica","Sit",4555),
+ SileneDioica("Silene dioica","Sd",39879),
+ SileneLatifolia("Silene latifolia","Sla",37657),
+ SimmondsiaChinensis("Simmondsia chinensis","Sch",3999),
+ SinningiaCardinalis("Sinningia cardinalis","Sic",189007),
+ SinopodophyllumHexandrum("Sinopodophyllum hexandrum","She",93608),
+ SkeletonemaMarinoi("Skeletonema marinoi", "Sm", 267567),
+ SolanumAculeatissimum("Solanum aculeatissimum","Scl",267265),
SolanumLycopersicum("Solanum lycopersicum", "Sl", "Tomato", 4081),
+ SolanumMelongena("Solanum melongena","Som",4111),
+ SolanumPennellii("Solanum pennellii","Spe",28526),
SolanumTuberosum("Solanum tuberosum", "St", "Potato", 4113),
- SkeletonemaMarinoi("Skeletonema marinoi", "Sm", 267567),
-
+ SolidagoCanadensis("Solidago canadensis","Soc",59297),
+ SorbusAucuparia("Sorbus aucuparia","Soa",36599),
SorexAraneus ("Sorex araneus", "Sa", "Shrew", 42254),
SorghumBicolor ("Sorghum bicolor", "Sb", "Sorghum", 4558),
+ SpirodelaPolyrhiza("Spirodela polyrhiza","Spo",29656),
+ SporobolusAlterniflorus("Sporobolus alterniflorus","Spa",29706),
+ StellariaMedia("Stellaria media","Stm",13274),
+ StigmatellaAurantiaca("Stigmatella aurantiaca","Sta",41),
+ StreptococcusMutans("Streptococcus mutans","Smu",1309),
+ StreptococcusPneumoniae("Streptococcus pneumoniae","Spn",1001746),
+ StreptomycesAntibioticus("Streptomyces antibioticus","San",1890),
+ StreptomycesGriseus("Streptomyces griseus","Sg",1911),
+ StrobilanthesCusia("Strobilanthes cusia","Scu",222567),
SusScrofa("Sus scrofa", "Ss", "Pig", 9823),
+ SyntrophotaleaAcetylenica("Syntrophotalea acetylenica","Sac",29542),
+ SyzygiumAromaticum("Syzygium aromaticum","Sar",219868),
+ TagetesErecta("Tagetes erecta","Te",13708),
+ TagetesPatula("Tagetes patula","Tp",55843),
+ TanacetumBalsamita("Tanacetum balsamita","Tb",301877),
+ TanacetumVulgare("Tanacetum vulgare","Tv",128002),
+ TaxusBaccata("Taxus baccata","Tba",25629),
+ TaxusBrevifolia("Taxus brevifolia","Tbr",46220),
+ TaxusChinensis("Taxus chinensis","Tch",29808),
+ TaxusCuspidata("Taxus cuspidata","Tcu",99806),
+ TellimaGrandiflora("Tellima grandiflora","Tg",29775),
+ TetradesmusObliquus("Tetradesmus obliquus","To",3088),
TetraodonNigroviridis ("Tetraodon nigroviridis", "Tn", "Pufferfish", 99883),
+ ThalassiosiraPseudonana("Thalassiosira pseudonana","Tps",35128),
+ ThalictrumFlavum("Thalictrum flavum","Tf",150094),
+ ThalictrumTuberosum("Thalictrum tuberosum","Tt",79802),
TheobromaCacao("Theobroma cacao", "Tc", "Cocoa", 3641),
+ ThermococcusKodakarensis("Thermococcus kodakarensis","Tk",311400),
+ ThermotogaMaritima("Thermotoga maritima","Tma",2336),
+ ThujaPlicata("Thuja plicata","Tpl",3316),
+ TrichosanthesKirilowii("Trichosanthes kirilowii","Tki",3677),
+ TrifoliumPratense("Trifolium pratense","Tpr",57577),
+ TrifoliumRepens("Trifolium repens","Tr",3899),
TriticumAestivum ("Triticum aestivum", "Ta", "Wheat", 4565),
+ TriticumSpelta("Triticum spelta","Ts",58933),
+ TriticumUrartu("Triticum urartu","Tu",4572),
+ UlvaIntestinalis("Ulva intestinalis","Ui",3116),
+ UlvaLactuca("Ulva lactuca","Ul",63410),
+ UrochloaPanicoides("Urochloa panicoides","Up",37563),
+ VacciniumMyrtillus("Vaccinium myrtillus","Vm",180763),
+ VanillaPlanifolia("Vanilla planifolia","Vp",51239),
+ VerniciaFordii("Vernicia fordii","Vf",73154),
+ VibrioCholerae("Vibrio cholerae","Vc",1225783),
+ VibrioFurnissii("Vibrio furnissii","Vfu",29494),
+ ViciaFaba("Vicia faba","Vfa",3906),
+ ViciaSativa("Vicia sativa","Vs",3908),
+ VignaAconitifolia("Vigna aconitifolia","Va",3918),
+ VignaAngularis("Vigna angularis","Van",3914),
+ VignaUnguiculata("Vigna unguiculata","Vu",3917),
VitisVinifera ("Vitis vinifera", "Vv", "Wine Grape", 29760),
+ WachendorfiaThyrsiflora("Wachendorfia thyrsiflora","Wt",95970),
+ XanthomonasArboricola("Xanthomonas arboricola","Xa",56448),
+ XanthomonasAxonopodis("Xanthomonas axonopodis","Xax",53413),
XenopusTropicalis("Xenopus tropicalis", "Xt", "Frog", 8364),
+ ZeaLuxurians("Zea luxurians","Zl",15945),
ZeaMays ("Zea mays", "Zm", "Maize", 4577),
+ ZingiberOfficinale("Zingiber officinale","Zo",94328),
+ ZingiberZerumbet("Zingiber zerumbet","Zz",311405),
+ ZymomonasMobilis("Zymomonas mobilis","Zmo",542),
;
private String latinName;
diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
index 812feb62d..cebedf6f7 100644
--- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
+++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
@@ -85,7 +85,7 @@ NCI Pathway Interaction Database Pid http://pid.nci.nih.gov/ http://pid.nci.nih.
OMIM Om http://omim.org/ http://omim.org/entry/$id 603903 gene 0 urn:miriam:mim ^[*#+%^]?\d{6}$ OMIM P492 omim gene,disease
OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ gene
ORCID orcid https://orcid.org https://orcid.org/$id 0000-0002-5355-2576 other Homo sapiens 1 urn:miriam:orcid ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ ORCID P496 orcid other,author
-Orphanet On http://www.orpha.net/consor/ https://identifiers.org/orphanet:$id 85163 other Homo sapiens 1 urn:miriam:orphanet ^\d+$ Bio2RDF orphanet other
+Orphanet On http://www.orpha.net/consor/ https://identifiers.org/orphanet:$id 85163 other Homo sapiens 1 urn:miriam:orphanet ^\d+$ Bio2RDF orpha other
Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob Oryzabase oryzabase.gene gene
Other O gene 1 O Other other
Pathway Commons Pc http://www.pathwaycommons.org/pc/ http://www.pathwaycommons.org/pc/record2.do?id=$id 485991 pathway 1 urn:miriam:pathwaycommons ^\d+$ Pathway Commons pathwaycommons pathway
@@ -123,7 +123,8 @@ SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/s
SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein
SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite
Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology
-TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene
+TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/locus?accession=$id 2200950 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^\d+$ TAIR Locus tair.locus gene
+TAIR gene name Agn https://www.arabidopsis.org/ https://www.arabidopsis.org/locus?name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.name ^AT[1-5]G\d{5}$ TAIR gene name araport gene
TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene
TTD Drug Td http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug ttd.drug metabolite
TTD Target Tt http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target ttd.target protein
diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv
index 940d8117d..415b7df5d 100644
--- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv
+++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv
@@ -1,54 +1,549 @@
genus species short name symbol ncbi
+Abies grandis Grand fir Abg 46611
+Acer pseudoplatanus Ap 4026
Acetobacterium woodii Aw 33952
+Acetobacter subgen. Acetobacter As 151157
+Acinetobacter baylyi Ab 202950
+Actinidia chinensis Acc 3625
+Actinidia deliciosa Ad 3627
+Actinidia eriantha Ae 165200
+Adiantum capillus-veneris Ac 13818
+Adonis aestivalis Ada 113211
+Adonis annua Aan 212759
+Aegilops tauschii Ata 37682
+Agapanthus africanus African lily Al 51501
+Albizia julibrissin Aj 3813
+Allium aflatunense Aaf 70752
+Allium altaicum Aal 48666
+Allium altyncolicum Ala 165602
+Allium ampeloprasum Aam 4681
+Allium ascalonicum Aas 1476995
+Allium cepa Ace 4679
+Allium chinense Ach 130426
+Allium fistulosum Af 35875
+Allium nutans Anu 138328
+Allium ochotense Ao 669879
+Allium sativum Asa 4682
+Allium schoenoprasum Asc 74900
+Allium tuberosum Atu 4683
+Allium ursinum Au 4684
+Allium victorialis Av 88845
+Aloe arborescens Aar 45385
+Aloe ferox Afe 117798
+Amaranthus cruentus Acr 117272
+Amaranthus hypochondriacus Ah 28502
+Amorpha fruticosa Afr 48131
+Anaerotignum propionicum Apr 28446
+Anchusa officinalis Ano 89630
+Anethum foeniculum Afo 2849586
+Anigozanthos preissii Anp 95948
+Anisodus acutangulus Aac 402998
Anopheles gambiae Mosquito Ag 7165
+Anthriscus sylvestris Asy 48027
+Antirrhinum majus Am 4151
+Aphelandra squarrosa Asq 103766
+Apium graveolens Agr 4045
+Aquifex aeolicus Aae 63363
+Aquilaria crassna Aqc 223751
+Aquilegia vulgaris Avu 3451
+Arabidopsis lyrata Aly 59689
Arabidopsis thaliana Arabidopsis At 3702
+Arachis hypogaea Ahy 3818
+Archaeoglobus fulgidus Afu 2234
+Artemisia annua Aa 35608
+Asclepias syriaca Ass 48545
+Asparagus officinalis Aof 4686
Aspergillus niger Black mold An 5061
+Aspergillus terricola Ate 36642
+Astragalus bisulcatus Abi 20406
+Atractylodes lancea Atl 41486
+Atropa belladonna Abe 33113
+Auxenochlorella pyrenoidosa Apy 3078
+Avena clauda Acl 83523
+Avena longiglumis Alo 4500
+Avena prostrata Avp 279683
+Avena sativa Avs 4498
+Avena strigosa Ast 38783
+Avena ventricosa Ave 146535
+Bacillus anthracis Ba 1392
Bacillus subtilis Bsubtilis Bs 1423
+Barnadesia spinosa Bsp 171760
+Batis maritima Bm 4436
+Berberis stolonifera Bst 33814
Beta vulgaris Sugar Beet Bv 3555
+Betula pubescens Bp 38787
+Bifidobacterium longum Bl 206672
+Bixa orellana Bor 66672
Bos taurus Cow Bt 9913
-Brassica napus Rapeseed Bn 3708
+Botryococcus braunii Bb 1202541
+Brassica juncea Bj 3707
+Brassica napus Rapeseed Bn 3708
+Brassica nigra Bni 3710
+Brassica oleracea Wild cabbage Bo 3712
+Brassica rapa Br 3711
+Bromus inermis Bi 15371
+Bruguiera gymnorhiza Bg 39984
Caenorhabditis elegans Celegans Ce 6239
+Camellia irrawadiensis Cir 153142
+Camellia ptilophylla Cpt 319931
+Camellia sinensis Cas 4442
+Camellia taliensis Cta 182317
+Camptotheca acuminata Cac 16922
+Canavalia ensiformis Cen 3823
+Canavalia lineata Cli 28957
Canis familiaris Dog Cf 9615
+Cannabis sativa Csa 3483
+Capsicum annuum Caa 4072
+Capsicum baccatum Cb 33114
+Capsicum chinense Cch 80379
+Capsicum frutescens Cfr 4073
+Carapichea ipecacuanha Cip 77880
+Carica papaya Cp 3649
+Carpobrotus acinaciformis Caa 1053334
+Carthamus tinctorius Cti 4222
+Carum carvi Cc 48032
+Catharanthus roseus Madagascar periwinkle Car 4058
+Caulobacter vibrioides Cv 155892
+Celosia cristata Ccr 124768
+Centaurium erythraea Cer 172057
+Cephalocereus senilis Cse 223054
+Cerastium arvense Cea 271558
+Ceratodon purpureus Cpu 3225
+Cereibacter sphaeroides Csp 1063
+Cestrum elegans Cel 103475
+Chelidonium majus Cm 71251
+Chlamydia trachomatis Ctr 759363
+Chlamydomonas reinhardtii Cr 3055
+Chrysanthemum × morifolium C× 41568
+Chrysosplenium americanum Cam 36749
+Cicer arietinum Chickpea Cia 3827
+Cichorium intybus Cin 13427
+Cinchona calisaya Cca 153742
+Cinchona macrocalyx Cma 273779
+Cinchona mutisii Cmu 273780
+Cinchona officinalis Co 273781
+Cinchona pitayensis Cpi 128294
+Cinchona pubescens Cpb 50278
+Cinnamomum tenuipile Cte 192326
Ciona intestinalis Sea Squirt Ci 7719
+Citrullus lanatus Cl 3654
+Citrus × aurantium Cxa 43166
+Citrus × clementina Cxc 85681
+Citrus hanaju Ch 481547
+Citrus japonica Cj 76966
+Citrus junos Cju 135197
+Citrus maxima Cim 37334
+Citrus × microcarpa Cmi 164113
+Citrus × paradisi Cxp 37656
+Citrus sinensis Sweet orange Cs 2711
+Citrus trifoliata Cit 37690
+Citrus unshiu Cun 55188
+Clarkia breweri Cbr 36903
+Cleretum bellidiforme Cbe 90527
+Clitoria ternatea Clt 43366
+Clostridium acetobutylicum Cla 1488
+Clostridium botulinum Cbo 1491
+Clostridium kluyveri Ck 1534
Clostridium thermocellum Cthe Ct 1515
-Caulobacter vibrioides Cv 155892
+Coffea abeokutae Cab 213304
+Coffea arabica Coffee Ca 13443
+Coffea canephora Coc 49390
+Coffea eugenioides Ceu 49369
+Coffea liberica Col 49373
+Coleus scutellarioides Csc 4142
+Consolida orientalis Cor 565971
+Coptis japonica Coj 3442
+Coptis teeta Cot 261448
+Corallococcus coralloides Cco 184914
+Coreopsis grandiflora Cg 13449
+Corydalis vaginans Cva 3044017
+Crambe hispanica Chi 70124
+Crepis palaestina Cpa 72611
+Crocus sativus Crs 82528
+Croton stellatopilosus Cst 431156
+Croton sublyratus Csu 107238
+Cryptomeria japonica Cja 3369
+Cucumis melo Muskmelon Cme 3656
+Cucumis sativus Cucumber Cu 3659
+Cucurbita maxima Cum 3661
+Cucurbita pepo Cpe 3663
+Curcuma longa Clo 136217
+Cyanidioschyzon merolae Cym 45157
+Cystobacter fuscus Cfu 43
+Cytophaga hutchinsonii Chu 985
+Dahlia pinnata Dpi 101596
Danio rerio Zebrafish Dr 7955
+Daphne odora Do 329675
Daphnia magna Da 35525
Daphnia pulex Dp 6669
Dasypus novemcinctus Armadillo Dn 9361
+Datura inoxia Di 4075
+Datura stramonium Dst 4076
+Daucus carota Dca 4039
+Davallia trichomanoides Dt 328206
+Delftia acidovorans Dac 80866
+Delphinium grandiflorum Dg 85439
+Derris elliptica De 56063
+Desmodium uncinatum Dun 225101
+Dianthus caryophyllus Dc 3570
+Dicranum scoparium Ds 3222
+Dictyostelium discoideum Dd 44689
+Digitalis lanata Dl 49450
+Digitalis purpurea Dpu 4164
+Diospyros kaki Dk 35925
+Dolichandra unguis-cati Du 73871
Drosophila melanogaster Fruitfly Dm 7227
Echinops telfairi Hedgehog Et 9371
+Enterococcus faecalis Ef 1351
+Equisetum arvense Ea 3258
Equus caballus Horse Qc 9796
+Erwinia amylovora Eam 552
+Erythroxylum coca Erc 289672
Escherichia coli Ecoli Ec 562
+Eschscholzia californica Eca 3467
+Eucalyptus piperita Ep 87677
+Euglena gracilis Eg 3039
+Euonymus alatus Eal 4307
+Euphorbia lagascae El 54672
+Eustoma grandiflorum Egr 52518
+Fagopyrum esculentum Fe 3617
+Fagopyrum tataricum Ft 62330
+Fagus crenata Fc 28929
+Felis catus Fca 9685
+Flaveria bidentis Fb 4224
+Flaveria chlorifolia Fch 4228
+Fluviicola taffensis Fta 191579
+Forsythia × intermedia F× 55183
+Forsythia koreana Fk 205692
+Fragaria × ananassa F× 3747
+Galanthus elwesii Ge 82232
+Galium mollugo Gmo 254777
Gallus gallus Chicken Gg 9031
-Glycine max Soybean Gm 3847
+Gardenia jasminoides Gj 114476
+Gemmata obscuriglobus Go 114
+Gentiana straminea Gs 50768
+Gentiana triflora Gt 55190
+Gerbera hybrid Ghy 18101
Gibberella zeae Fusarium graminearum Gz 5518
+Ginkgo biloba Gb 3311
+Glandularia × hybrida G× 76714
+Glebionis segetum Gse 118509
+Glycine max Soybean Gm 3847
+Glycyrrhiza echinata Gec 46348
+Glycyrrhiza glabra Liquorice Gl 49827
+Gossypium arboreum Ga 29729
+Gossypium barbadense Gba 3634
+Gossypium hirsutum Ghi 3635
+Guatteria blepharophylla Gbl 402568
+Guatteria friesiana Gf 402569
+Guatteria hispida Gh 402570
+Haematococcus lacustris Hl 44745
+Halobacterium salinarum Hsa 2242
+Haloferax volcanii Hvo 2246
+Helianthus annuus Ha 4232
+Helianthus tuberosus Ht 4233
+Helicobacter pylori Hp 210
+Hevea brasiliensis Hb 3981
Homo sapiens Human Hs 9606
+Hordeum lechleri Hle 38856
Hordeum vulgare Barley Hv 4513
+Hydrangea macrophylla Hm 23110
+Hyoscyamus albus Hal 310458
+Hyoscyamus muticus Hmu 35626
+Hyoscyamus niger Hn 4079
+Hypericum androsaemum Han 140968
+Hypericum calycinum Hc 55963
+Hypericum perforatum Hpe 65561
+Hyphomicrobium zavarzinii Hz 48292
+Ilex paraguariensis Yerba mate Ip 185542
+Impatiens balsamina Ib 63779
+Ipomoea batatas Iba 4120
+Ipomoea nil In 35883
+Ipomoea purpurea Ipu 4121
+Juglans regia Jr 51240
+Kandelia candel Kc 61147
+Klebsiella oxytoca Ko 571
+Klebsiella pneumoniae Kp 1284798
+Lacticaseibacillus casei Lc 1312920
+Lactococcus lactis Ll 1358
+Lactuca sativa Ls 4236
+Lamium galeobdolon Lg 53161
+Lathyrus odoratus Lo 3859
+Lathyrus oleraceus Garden Pea Ps 3888
+Lavandula angustifolia Laa 39329
+Lawsonia inermis Li 141191
+Lemna aequinoctialis Lae 89585
+Lemna minor Lm 4472
+Lens culinaris Lcu 3864
+Leucaena leucocephala Lle 3866
+Lilium longiflorum Llo 4690
+Limnanthes alba Lal 42439
+Limnanthes douglasii Ld 28973
+Limonium latifolium Lla 227291
+Linum flavum Lf 407263
+Linum nodiflorum Ln 407264
+Linum perenne Lp 35941
+Linum usitatissimum Lu 4006
+Lithospermum erythrorhizon Le 34254
+Lotus corniculatus Lco 47247
+Lotus japonicus Lj 34305
Loxodonta africana Elephant La 9785
+Lunaria annua Lan 153659
+Lupinus albus Lua 3870
+Lupinus luteus Yellow lupine Llu 3873
+Lupinus polyphyllus Lpo 3874
+Lygodium circinatum Lci 84615
Macaca mulatta Rhesus Monkey Ml 9544
+Magnolia grandiflora Mg 3406
+Magnolia obovata Mo 349509
+Malus domestica Apple Mad 3750
+Malus hupehensis Mh 106556
+Malus pumila Mp 283210
+Manihot esculenta Cassava Me 3983
+Matthiola incana Mi 3724
+Medicago sativa Alfalfa Ma 3879
+Megathyrsus maximus Mma 59788
+Melilotus albus Mal 47082
+Mentha aquatica Maq 190902
+Mentha × gracilis M× 241069
+Mentha × piperita M× 34256
+Mentha spicata Ms 29719
+Methanocaldococcus jannaschii Mj 2190
+Methanosarcina mazei Mem 1434114
+Methanosarcina thermophila Mt 2210
+Methanothermobacter marburgensis Mmb 145263
+Methyloceanibacter caenitepidi Mc 1384459
+Methylococcus capsulatus Mca 414
+Methylorubrum extorquens Mex 408
+Methylosphaera hansonii Mha 51353
+Micrococcus luteus Mlu 1270
+Mirabilis jalapa Mja 3538
+Momordica charantia Mch 3673
Monodelphis domestica Opossum Md 13616
+Musa acuminata Mac 4641
Mus musculus Mouse Mm 10090
+Mycobacterium avium Mav 1764
+Mycobacterium kansasii Mk 1768
Mycobacterium tuberculosis Mtuberculosis Mx 1773
+Mycolicibacterium fortuitum Mf 1766
+Mycolicibacterium phlei Mph 1771
+Mycoplasmoides pneumoniae Mpn 1263835
+Nannocystis exedens Ne 54
+Narcissus pseudonarcissus Nps 39639
+Nepenthes alata Na 4376
+Nepenthes gracilis Ng 150966
+Nepenthes mirabilis Nm 150983
+Nepenthes rafflesiana Nra 150990
+Nerine bowdenii Nb 59042
+Neurospora crassa Nc 5141
+Nicotiana attenuata Nat 49451
+Nicotiana benthamiana Nbe 4100
+Nicotiana glutinosa Ngl 35889
+Nicotiana plumbaginifolia Np 4092
+Nicotiana rustica Nr 4093
+Nicotiana sylvestris Ns 4096
+Nicotiana tabacum Tabacco Nt 4097
+Nitrosopumilus maritimus Nma 338192
+Nothapodytes nimmoniana Nn 159386
+Ocimum basilicum Basil Ob 39350
+Olea europaea Oe 4146
+Ophiorrhiza japonica Opj 367363
+Ophiorrhiza pumila Op 157934
Ornithorhynchus anatinus Platypus Oa 9258
Oryctolagus cuniculus Rabbit Oc 9986
Oryza sativa Japanese Rice Os 4530
Oryzias latipes Medaka Fish Ol 8090
Ovis aries sheep Ova 9940
+Oxybasis rubra Or 3560
+Panax ginseng Pgi 4054
+Panax notoginseng Pno 44586
+Panicum miliaceum Pm 4540
+Panicum virgatum Pvi 38727
+Pantoea agglomerans Pag 549
+Pantoea ananatis Paa 553
Pan troglodytes Chimp Pt 9598
+Papaver somniferum Opium poppy Pas 3469
+Passiflora edulis Ped 78168
+Paullinia cupana Guarana Pc 392747
+Pelargonium crispum Pcr 1417776
+Pericallis cruenta Pec 98709
+Perilla frutescens Beefsteak plant Pe 48386
+Persea americana Pa 3435
+Persicaria tinctoria Pti 96455
+Petiveria alliacea Pal 46142
+Petroselinum crispum Pcs 4043
+Petunia x hybrida Pxh 4102
+Phaseolus coccineus Pco 3886
+Phaseolus lunatus Plu 3884
+Phaseolus vulgaris Common bean Pv 3885
+Phlebodium aureum Pau 218620
+Phleum pratense Ppr 15957
+Phragmites australis Phu 29695
+Physaria fendleri Pfe 63442
+Physaria lindheimeri Pl 439687
+Physcomitrium patens Pha 3218
+Picea abies Norway spruce Pia 3329
+Picea glauca Pg 3330
+Pimpinella anisum Pan 271192
+Pinus banksiana Pb 3353
+Pinus contorta Pic 3339
+Pinus densiflora Pde 77912
+Pinus ponderosa Ppo 55062
+Pinus sabiniana Psa 268869
+Pinus strobus Pst 3348
+Pinus sylvestris Psy 3349
+Pinus taeda Loblolly pine Pit 3352
+Plantago major Pma 29818
Plasmodium falciparum Malaria parasite Pf 5833
-Prymnesium parvum Pp 97485
+Plectranthus barbatus Pba 41228
+Plumbago europaea Peu 114226
+Plumbago indica Pin 122308
+Podophyllum peltatum Ppe 35933
+Pogostemon cablin Pca 28511
+Polaribacter filamentus Pfi 53483
+Populus alba Poa 43335
+Populus deltoides Pod 3696
+Populus nigra Pni 3691
Populus trichocarpa Western Balsam Poplar Pi 3694
+Portulaca grandiflora Pog 3583
+Prunus dulcis Pd 3755
+Prunus mume Pmu 102107
+Prymnesium parvum Pp 97485
+Pseudomonas aeruginosa Pae 1009714
+Pseudomonas fluorescens Pfl 294
+Psilotum nudum Pn 3240
+Pteris vittata Ptv 13821
+Pueraria montana Pmo 132459
+Punica granatum Pgr 22663
+Pyrus pyrifolia Ppy 3767
+Quercus robur Qro 38942
+Quercus rubra Qr 3512
+Raphanus sativus Rsa 3726
Rattus norvegicus Rat Rn 10116
+Rheum palmatum Rp 137221
+Rheum tataricum Rt 205071
+Rhizophora apiculata Ra 106626
+Rhizophora mangle Rm 40031
+Rhizophora stylosa Rst 98588
+Rhodiola rosea Rr 203015
+Rhodiola sachalinensis Rs 265354
+Rhodobacter capsulatus Rca 1061
+Rhodotorula glutinis Rgl 5535
+Rhus typhina Rty 255348
+Ricinus communis Castor bean Ri 3988
+Robinia pseudoacacia Rps 35938
+Rosa chinensis Rc 74649
+Rosa hybrid Rhy 128735
Rosmarinus officinalis Rosemary Ro 39367
+Rubia tinctorum Rti 29802
+Rubus idaeus Rid 32247
+Rudbeckia hirta Rh 52299
+Ruta graveolens Rg 37565
Saccharomyces cerevisiae Yeast Sc 4932
+Saccharopolyspora spinosa Ssp 60894
+Saccharum officinarum Sof 4547
+Salmonella enterica Se 28901
+Salvia fruticosa Greek sage Sf 268906
+Salvia fruticosa Sfr 268906
+Salvia officinalis Sao 38868
+Salvia rosmarinus Sr 39367
+Salvia splendens Spl 180675
+Sanguinaria canadensis Sca 3472
+Santalum album Saa 35974
+Santalum austrocaledonicum Sau 293154
+Santalum spicatum Sas 453088
+Sarcina ventriculi Sv 1267
+Saussurea medusa Sme 137893
+Saxifraga stolonifera Sst 182070
+Schizonepeta tenuifolia Ste 2849020
+Schizosaccharomyces pombe Sp 4896
+Scutellaria baicalensis Sba 65409
+Scutellaria viscidula Svi 512023
+Secale cereale Sce 4550
+Selaginella lepidophylla Sle 59777
+Senecio vernalis Sve 93496
+Senecio vulgaris Svu 76276
+Serratia marcescens Sma 1401254
+Sesamum alatum Sal 300844
+Sesamum indicum Si 4182
+Sesamum radiatum Sra 300843
+Sesbania rostrata Sro 3895
+Setaria italica Sit 4555
+Silene dioica Sd 39879
+Silene latifolia Sla 37657
+Simmondsia chinensis Sch 3999
+Sinningia cardinalis Sic 189007
+Sinopodophyllum hexandrum She 93608
Skeletonema marinoi Sm 267567
+Solanum aculeatissimum Scl 267265
+Solanum habrochaites Sh 62890
Solanum lycopersicum Tomato Sl 4081
-Solanum tuberosum St 4113
+Solanum melongena Som 4111
+Solanum pennellii Spe 28526
+Solanum tuberosum Potato St 4113
+Solidago canadensis Soc 59297
+Sorbus aucuparia Soa 36599
Sorex araneus Shrew Sa 42254
Sorghum bicolor Sorghum Sb 4558
+Spinacia oleracea Spinach So 3562
+Spirodela polyrhiza Spo 29656
+Sporobolus alterniflorus Spa 29706
+Stellaria media Stm 13274
+Stigmatella aurantiaca Sta 41
+Streptococcus mutans Smu 1309
+Streptococcus pneumoniae Spn 1001746
+Streptomyces antibioticus San 1890
+Streptomyces griseus Sg 1911
+Strobilanthes cusia Scu 222567
Sus scrofa Pig Ss 9823
+Syntrophotalea acetylenica Sac 29542
+Syzygium aromaticum Sar 219868
+Tagetes erecta Te 13708
+Tagetes patula Tp 55843
+Tanacetum balsamita Tb 301877
+Tanacetum vulgare Tv 128002
+Taxus baccata Tba 25629
+Taxus brevifolia Tbr 46220
+Taxus chinensis Tch 29808
+Taxus cuspidata Tcu 99806
+Tellima grandiflora Tg 29775
+Tetradesmus obliquus To 3088
Tetraodon nigroviridis Pufferfish Tn 99883
+Thalassiosira pseudonana Tps 35128
+Thalictrum flavum Tf 150094
+Thalictrum tuberosum Tt 79802
+Theobroma cacao Cocoa Tc 3641
+Thermococcus kodakarensis Tk 311400
+Thermotoga maritima Tma 2336
+Thuja plicata Tpl 3316
+Trichosanthes kirilowii Tki 3677
+Trifolium pratense Tpr 57577
+Trifolium repens Tr 3899
+Triglochin maritima Tm 55501
+Triticum spelta Ts 58933
+Triticum urartu Tu 4572
+Ulva curvata Green algea Uc 135247
+Ulva intestinalis Ui 3116
+Ulva lactuca Ul 63410
+Urochloa panicoides Up 37563
+Vaccinium myrtillus Vm 180763
+Vanilla planifolia Vp 51239
+Vernicia fordii Vf 73154
+Vibrio cholerae Vc 1225783
+Vibrio furnissii Vfu 29494
+Vicia faba Vfa 3906
+Vicia sativa Vs 3908
+Vigna aconitifolia Va 3918
+Vigna angularis Van 3914
+Vigna radiata Vr 157791
+Vigna unguiculata Vu 3917
Vitis vinifera Wine Grape Vv 29760
+Wachendorfia thyrsiflora Wt 95970
+Xanthomonas arboricola Xa 56448
+Xanthomonas axonopodis Xax 53413
Xenopus tropicalis Xenopus Xt 8364
+Zea luxurians Zl 15945
Zea mays Maize Zm 4577
+Zingiber officinale Zo 94328
+Zingiber zerumbet Zz 311405
+Zymomonas mobilis Zmo 542
diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml
index 51c0427d5..879fdcab5 100644
--- a/org.bridgedb.gui/pom.xml
+++ b/org.bridgedb.gui/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml
index f3846c62c..386d915f8 100644
--- a/org.bridgedb.rdb.construct/pom.xml
+++ b/org.bridgedb.rdb.construct/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml
index 6627c385b..042992a64 100644
--- a/org.bridgedb.rdb/pom.xml
+++ b/org.bridgedb.rdb/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java b/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java
index 7fb4e2dfd..7aa861b46 100644
--- a/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java
+++ b/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java
@@ -91,12 +91,19 @@ public IDMapper connect(String location) throws IDMapperException
String port = args.containsKey("port") ? args.get("port") : "1527";
try {
- Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4
- System.out.println("Derby ClientDriver loaded");
+ Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4
+ System.out.println("Derby ClientDriver loaded (for Derby 10.4)");
} catch (ClassNotFoundException e) {
// ignore, probably we're running this with Derby 10.14 or higher
}
- Properties sysprop = System.getProperties();
+ try {
+ Class.forName("org.apache.derby.jdbc.EmbeddedDriver"); // Derby 10.14 or higher
+ System.out.println("Derby ClientDriver loaded (for Derby 10.14+)");
+ } catch (ClassNotFoundException e) {
+ // ignore, probably we're running this with Derby lower than 10.14
+ }
+
+ Properties sysprop = System.getProperties();
sysprop.setProperty("derby.storage.tempDirectory", System.getProperty("java.io.tmpdir"));
sysprop.setProperty("derby.stream.error.file", File.createTempFile("derby",".log").toString());
diff --git a/org.bridgedb.rdb/src/org/bridgedb/rdb/SimpleGdbImplCommon.java b/org.bridgedb.rdb/src/org/bridgedb/rdb/SimpleGdbImplCommon.java
index d2997281b..3b1a2b1f3 100644
--- a/org.bridgedb.rdb/src/org/bridgedb/rdb/SimpleGdbImplCommon.java
+++ b/org.bridgedb.rdb/src/org/bridgedb/rdb/SimpleGdbImplCommon.java
@@ -239,7 +239,7 @@ public Set freeSearch (String text, int limit) throws IDMapperException
* @return a list of data sources present in this database.
@throws IDMapperException when the database is unavailable
*/
- private Set getDataSources() throws IDMapperException
+ public Set getDataSources() throws IDMapperException
{
Set result = new HashSet();
final QueryLifeCycle pst = qDatasources;
diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml
index cf92dd303..147650892 100644
--- a/org.bridgedb.rdf/pom.xml
+++ b/org.bridgedb.rdf/pom.xml
@@ -6,7 +6,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl
index 0769394f8..40931c961 100644
--- a/org.bridgedb.rdf/resources/DataSource.ttl
+++ b/org.bridgedb.rdf/resources/DataSource.ttl
@@ -1069,7 +1069,7 @@ bridgeDB:DataSource_TAIR a bridgeDB:DataSource ;
bridgeDB:idExample "AT1G01030" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern .
bridgeDB:DataSource_TIGR a bridgeDB:DataSource ;
diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
index f8d76d0fd..4ac34aff8 100644
--- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
+++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
@@ -5761,7 +5761,7 @@ bridgeDB:DataSource_TAIR a bridgeDB:DataSource ;
bridgeDB:idExample "AT1G01030" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^AT[1-5]G\\d{5}$" ;
@@ -6862,8 +6862,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ;
a bridgeDB:UriPattern ;
bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?accession=" .
- a bridgeDB:UriPattern ;
- bridgeDB:hasPrefix "https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=" .
+ a bridgeDB:UriPattern ;
+ bridgeDB:hasPrefix "https://www.arabidopsis.org/locus?accession=" .
a bridgeDB:UriPattern ;
bridgeDB:hasPrefix "http://arxiv.org/abs/" .
diff --git a/org.bridgedb.rdf/resources/MiriamRegistry.ttl b/org.bridgedb.rdf/resources/MiriamRegistry.ttl
index c8902446c..a1655956f 100644
--- a/org.bridgedb.rdf/resources/MiriamRegistry.ttl
+++ b/org.bridgedb.rdf/resources/MiriamRegistry.ttl
@@ -7057,7 +7057,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus
a dcat:Distribution ;
- dcat:accessURL ;
+ dcat:accessURL ;
dcat:mediaType "application/xhtml+xml"^^ ;
dcat:publisher .
diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml
index 3a027918e..2b762c9ab 100644
--- a/org.bridgedb.sql/pom.xml
+++ b/org.bridgedb.sql/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml
index 13c70b14f..f9cc04eee 100644
--- a/org.bridgedb.tools.batchmapper/pom.xml
+++ b/org.bridgedb.tools.batchmapper/pom.xml
@@ -6,7 +6,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
@@ -33,19 +33,19 @@
org.bridgedb
org.bridgedb
- 3.0.29
+ 3.0.30
compile
org.bridgedb
org.bridgedb.bio
- 3.0.29
+ 3.0.30
compile
org.bridgedb
org.bridgedb.rdb
- 3.0.29
+ 3.0.30
compile
diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml
index e641cbded..d0166c227 100644
--- a/org.bridgedb.tools.info/pom.xml
+++ b/org.bridgedb.tools.info/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml
index 0ebf2e9f8..3e0a4435d 100644
--- a/org.bridgedb.tools.qc/pom.xml
+++ b/org.bridgedb.tools.qc/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
@@ -32,6 +32,7 @@
org.apache.maven.plugins
maven-assembly-plugin
+ ${maven-assembly.version}
package
diff --git a/org.bridgedb.tools.qc/src/org/bridgedb/tools/qc/BridgeQC.java b/org.bridgedb.tools.qc/src/org/bridgedb/tools/qc/BridgeQC.java
index 85defb98e..49cdc9eb8 100644
--- a/org.bridgedb.tools.qc/src/org/bridgedb/tools/qc/BridgeQC.java
+++ b/org.bridgedb.tools.qc/src/org/bridgedb/tools/qc/BridgeQC.java
@@ -76,6 +76,19 @@ public BridgeQC(File f1, File f2, OutputStream out) throws IDMapperException
public void initDatabases() throws IDMapperException
{
+ try {
+ Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4
+ System.out.println("Derby ClientDriver loaded (for Derby 10.4)");
+ } catch (ClassNotFoundException e) {
+ // ignore, probably we're running this with Derby 10.14 or higher
+ }
+ try {
+ Class.forName("org.apache.derby.jdbc.EmbeddedDriver"); // Derby 10.14 or higher
+ System.out.println("Derby ClientDriver loaded (for Derby 10.14+)");
+ } catch (ClassNotFoundException e) {
+ // ignore, probably we're running this with Derby lower than 10.14
+ }
+
String url1 = "jdbc:derby:jar:(" + oldDb + ")database";
oldGdb = SimpleGdbFactory.createInstance("old", url1);
this.out.printf("INFO: old database is %s %s (build: %s)\n",
diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml
index 68d62c0d5..c55f2589c 100644
--- a/org.bridgedb.tools.voidtool/pom.xml
+++ b/org.bridgedb.tools.voidtool/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
@@ -32,6 +32,7 @@
org.apache.maven.plugins
maven-assembly-plugin
+ ${maven-assembly.version}
package
diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml
index bfdc43a10..f29333901 100644
--- a/org.bridgedb.uri.api/pom.xml
+++ b/org.bridgedb.uri.api/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml
index ef7144267..de3062ec1 100644
--- a/org.bridgedb.uri.loader/pom.xml
+++ b/org.bridgedb.uri.loader/pom.xml
@@ -6,7 +6,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml
index 66816704f..9f790a9d0 100644
--- a/org.bridgedb.uri.sql/pom.xml
+++ b/org.bridgedb.uri.sql/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml
index 008e8e5f0..150568b2a 100644
--- a/org.bridgedb.uri.ws.client/pom.xml
+++ b/org.bridgedb.uri.ws.client/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml
index 1aeeb4bc4..f5d95d949 100644
--- a/org.bridgedb.uri.ws.core/pom.xml
+++ b/org.bridgedb.uri.ws.core/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml
index 576a2cdd1..532b229c3 100644
--- a/org.bridgedb.uri.ws.server/pom.xml
+++ b/org.bridgedb.uri.ws.server/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml
index c37b1c386..8ad73a694 100644
--- a/org.bridgedb.utils/pom.xml
+++ b/org.bridgedb.utils/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml
index 841c412bf..fac0ba12a 100644
--- a/org.bridgedb.webservice.biomart/pom.xml
+++ b/org.bridgedb.webservice.biomart/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml
index a27444575..19eef5f33 100644
--- a/org.bridgedb.webservice.bridgerest/pom.xml
+++ b/org.bridgedb.webservice.bridgerest/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml
index 80cf42085..88b0c2a5e 100644
--- a/org.bridgedb.ws.client/pom.xml
+++ b/org.bridgedb.ws.client/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml
index 1aec28604..211aa60d7 100644
--- a/org.bridgedb.ws.core/pom.xml
+++ b/org.bridgedb.ws.core/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml
index 02121089c..c08f44186 100644
--- a/org.bridgedb.ws.server/pom.xml
+++ b/org.bridgedb.ws.server/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml
index c8b8cc086..aeb3f7876 100644
--- a/org.bridgedb/pom.xml
+++ b/org.bridgedb/pom.xml
@@ -8,7 +8,7 @@
org.junit.platform
junit-platform-surefire-provider
- 1.3.2
+ ${junit-platform-surefire-provider}
test
@@ -38,7 +38,7 @@
bridgedb-bundle
org.bridgedb
- 3.0.29
+ 3.0.30
diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props
index 1618b590f..dfd386fab 100644
--- a/org.bridgedb/src/main/resources/version.props
+++ b/org.bridgedb/src/main/resources/version.props
@@ -1,2 +1,2 @@
# Current version of BridgeDb
-bridgedb.version=3.0.29
+bridgedb.version=3.0.30
diff --git a/pom.xml b/pom.xml
index 725cb2b9b..4c8ec4e47 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
org.bridgedb
bridgedb-bundle
pom
- 3.0.29
+ 3.0.30
BridgeDb bundle
BridgeDb is a framework for finding and mapping equivalent database
@@ -48,20 +48,21 @@
5.1.9
3.0
1.10
- 2.20.0
- 9.0.0
+ 2.25.3
+ 9.5.0
Tomcat
3.4
4.3.8
2.5
2.0.9
10.15.2.0
- 33.4.8-jre
+ 33.5.0-jre
- 3.4.2
+ 3.5.0
+ 3.8.0
1.3.2
- 1.11.0
- 5.11.0
+ 1.14.1
+ 5.14.1
mysql
@@ -71,7 +72,7 @@
maven-compiler-plugin
- 3.8.1
+ 3.14.1
8
8
@@ -100,7 +101,7 @@
org.apache.maven.plugins
maven-source-plugin
- 3.2.1
+ 3.4.0
attach-sources
@@ -114,7 +115,7 @@
org.apache.maven.plugins
maven-surefire-plugin
- 2.22.2
+ 2.22.0
false
1
@@ -125,7 +126,7 @@
org.jacoco
jacoco-maven-plugin
- 0.8.4
+ 0.8.14
start-agent
@@ -151,7 +152,7 @@
org.sonatype.central
central-publishing-maven-plugin
- 0.8.0
+ 0.9.0
true
central
@@ -162,7 +163,7 @@
org.apache.maven.plugins
maven-gpg-plugin
- 1.6
+ 3.2.8
sign-artifacts
@@ -176,7 +177,7 @@
org.apache.maven.plugins
maven-javadoc-plugin
- 3.4.0
+ 3.12.0
-Xdoclint:none
8
@@ -193,7 +194,7 @@
org.apache.maven.plugins
maven-enforcer-plugin
- 3.5.0
+ 3.6.2
enforce-maven