bio 2.0.3 → 2.0.5

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Files changed (32) hide show
  1. checksums.yaml +4 -4
  2. data/.github/workflows/ruby.yml +38 -0
  3. data/.gitignore +32 -0
  4. data/ChangeLog +366 -0
  5. data/Gemfile +3 -0
  6. data/LEGAL +11 -0
  7. data/README.rdoc +1 -1
  8. data/RELEASE_NOTES.rdoc +50 -0
  9. data/appveyor.yml +14 -13
  10. data/bioruby.gemspec +9 -10
  11. data/lib/bio/appl/blast/genomenet.rb +2 -1
  12. data/lib/bio/appl/pts1.rb +1 -1
  13. data/lib/bio/db/embl/uniprotkb.rb +184 -26
  14. data/lib/bio/version.rb +1 -1
  15. data/test/data/uniprot/P03589.uniprot +127 -0
  16. data/test/data/uniprot/P28907.uniprot +551 -0
  17. data/test/data/uniprot/P49144.uniprot +232 -0
  18. data/test/functional/bio/test_command.rb +2 -0
  19. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +26 -12
  20. data/test/unit/bio/db/embl/test_uniprotkb_P03589.rb +378 -0
  21. data/test/unit/bio/db/embl/test_uniprotkb_P28907.rb +325 -0
  22. data/test/unit/bio/db/embl/test_uniprotkb_P49144.rb +359 -0
  23. metadata +14 -15
  24. data/.travis.yml +0 -71
  25. data/gemfiles/Gemfile.travis-jruby1.8 +0 -6
  26. data/gemfiles/Gemfile.travis-jruby1.9 +0 -5
  27. data/gemfiles/Gemfile.travis-rbx +0 -10
  28. data/gemfiles/Gemfile.travis-ruby1.8 +0 -6
  29. data/gemfiles/Gemfile.travis-ruby1.9 +0 -5
  30. data/gemfiles/Gemfile.windows +0 -6
  31. data/gemfiles/modify-Gemfile.rb +0 -28
  32. data/gemfiles/prepare-gemspec.rb +0 -29
data/test/data/uniprot/P49144.uniprot ADDED
@@ -0,0 +1,232 @@
1
+ ID 5HT1B_RABIT Reviewed; 390 AA.
2
+ AC P49144;
3
+ DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
4
+ DT 01-FEB-1996, sequence version 1.
5
+ DT 22-FEB-2023, entry version 127.
6
+ DE RecName: Full=5-hydroxytryptamine receptor 1B;
7
+ DE Short=5-HT-1B;
8
+ DE Short=5-HT1B;
9
+ DE AltName: Full=Serotonin 1D beta receptor;
10
+ DE Short=5-HT-1D-beta;
11
+ DE AltName: Full=Serotonin receptor 1B;
12
+ GN Name=HTR1B;
13
+ OS Oryctolagus cuniculus (Rabbit).
14
+ OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
15
+ OC Eutheria; Euarchontoglires; Glires; Lagomorpha; Leporidae; Oryctolagus.
16
+ OX NCBI_TaxID=9986;
17
+ RN [1]
18
+ RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
19
+ RC TISSUE=Liver;
20
+ RX PubMed=8543023; DOI=10.1016/0014-5793(95)01308-3;
21
+ RA Harwood G.S., Lockyer M., Giles H., Fairweather N.;
22
+ RT "Cloning and characterisation of the rabbit 5-HT1D alpha and 5-HT1D beta
23
+ RT receptors.";
24
+ RL FEBS Lett. 377:73-76(1995).
25
+ RN [2]
26
+ RP NUCLEOTIDE SEQUENCE.
27
+ RC STRAIN=New Zealand white; TISSUE=Saphenous vein;
28
+ RA Wurch T., Cathala C., Palmer C., Valentin J.P., John G., Colpaert F.C.,
29
+ RA Pauwels P.J.;
30
+ RT "Molecular cloning and identification of a rabbit saphenous vein 5-HT 1DB
31
+ RT receptor gene.";
32
+ RL Neurosci. Res. Commun. 18:155-162(1996).
33
+ RN [3]
34
+ RP NUCLEOTIDE SEQUENCE.
35
+ RC STRAIN=New Zealand white;
36
+ RX PubMed=8878052; DOI=10.1007/bf00171053;
37
+ RA Bard J.A., Kucharewicz S.A., Zgombick J.M., Weinshank R.L., Branchek T.A.,
38
+ RA Cohen M.L.;
39
+ RT "Differences in ligand binding profiles between cloned rabbit and human 5-
40
+ RT HT1D alpha and 5-HT1D beta receptors: ketanserin and methiothepin
41
+ RT distinguish rabbit 5-HT1D receptor subtypes.";
42
+ RL Naunyn Schmiedebergs Arch. Pharmacol. 354:237-244(1996).
43
+ CC -!- FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine
44
+ CC (serotonin). Also functions as a receptor for various alkaloids and
45
+ CC psychoactive substances. Ligand binding causes a conformation change
46
+ CC that triggers signaling via guanine nucleotide-binding proteins (G
47
+ CC proteins) and modulates the activity of down-stream effectors, such as
48
+ CC adenylate cyclase. Signaling inhibits adenylate cyclase activity.
49
+ CC Arrestin family members inhibit signaling via G proteins and mediate
50
+ CC activation of alternative signaling pathways. Regulates the release of
51
+ CC 5-hydroxytryptamine, dopamine and acetylcholine in the brain, and
52
+ CC thereby affects neural activity, nociceptive processing, pain
53
+ CC perception, mood and behavior. Besides, plays a role in
54
+ CC vasoconstriction of cerebral arteries.
55
+ CC -!- SUBUNIT: Homodimer. Heterodimer with HTR1D (By similarity).
56
+ CC {ECO:0000250}.
57
+ CC -!- SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
58
+ CC -!- DOMAIN: Ligands are bound in a hydrophobic pocket formed by the
59
+ CC transmembrane helices. {ECO:0000250}.
60
+ CC -!- PTM: Phosphorylated. {ECO:0000250}.
61
+ CC -!- PTM: Palmitoylated. {ECO:0000250}.
62
+ CC -!- MISCELLANEOUS: A residue in the 7th transmembrane region ('Thr-355' in
63
+ CC human, 'Asn-351' in mouse and rat) is important for species-specific
64
+ CC sensitivity to various agonists. {ECO:0000250}.
65
+ CC -!- SIMILARITY: Belongs to the G-protein coupled receptor 1 family.
66
+ CC {ECO:0000255|PROSITE-ProRule:PRU00521}.
67
+ CC ---------------------------------------------------------------------------
68
+ CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
69
+ CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
70
+ CC ---------------------------------------------------------------------------
71
+ DR EMBL; Z50163; CAA90531.1; -; Genomic_DNA.
72
+ DR EMBL; X89731; CAA61883.1; -; mRNA.
73
+ DR EMBL; U60826; AAB58467.1; -; Genomic_DNA.
74
+ DR PIR; S58126; S58126.
75
+ DR PIR; S68422; S68422.
76
+ DR RefSeq; NP_001076259.1; NM_001082790.1.
77
+ DR AlphaFoldDB; P49144; -.
78
+ DR SMR; P49144; -.
79
+ DR STRING; 9986.ENSOCUP00000016295; -.
80
+ DR BindingDB; P49144; -.
81
+ DR ChEMBL; CHEMBL5717; -.
82
+ DR GlyCosmos; P49144; 2 sites, No reported glycans.
83
+ DR GeneID; 100009594; -.
84
+ DR KEGG; ocu:100009594; -.
85
+ DR CTD; 3351; -.
86
+ DR eggNOG; KOG3656; Eukaryota.
87
+ DR InParanoid; P49144; -.
88
+ DR OrthoDB; 2999405at2759; -.
89
+ DR TreeFam; TF316350; -.
90
+ DR PRO; PR:P49144; -.
91
+ DR Proteomes; UP000001811; Unplaced.
92
+ DR GO; GO:0005886; C:plasma membrane; ISS:UniProtKB.
93
+ DR GO; GO:0045202; C:synapse; IEA:GOC.
94
+ DR GO; GO:0004993; F:G protein-coupled serotonin receptor activity; ISS:UniProtKB.
95
+ DR GO; GO:0007198; P:adenylate cyclase-inhibiting serotonin receptor signaling pathway; ISS:UniProtKB.
96
+ DR GO; GO:0007610; P:behavior; IEA:UniProtKB-KW.
97
+ DR GO; GO:0046849; P:bone remodeling; IEA:InterPro.
98
+ DR GO; GO:0071312; P:cellular response to alkaloid; ISS:UniProtKB.
99
+ DR GO; GO:0071466; P:cellular response to xenobiotic stimulus; ISS:UniProtKB.
100
+ DR GO; GO:0007268; P:chemical synaptic transmission; IEA:InterPro.
101
+ DR GO; GO:0014063; P:negative regulation of serotonin secretion; ISS:UniProtKB.
102
+ DR GO; GO:0050795; P:regulation of behavior; IEA:InterPro.
103
+ DR GO; GO:0042310; P:vasoconstriction; IEA:InterPro.
104
+ DR CDD; cd15333; 7tmA_5-HT1B_1D; 1.
105
+ DR Gene3D; 1.20.1070.10; Rhodopsin 7-helix transmembrane proteins; 1.
106
+ DR InterPro; IPR002147; 5HT1B_rcpt.
107
+ DR InterPro; IPR002231; 5HT_rcpt.
108
+ DR InterPro; IPR000276; GPCR_Rhodpsn.
109
+ DR InterPro; IPR017452; GPCR_Rhodpsn_7TM.
110
+ DR PANTHER; PTHR24248; ADRENERGIC RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR; 1.
111
+ DR PANTHER; PTHR24248:SF66; OCTOPAMINE RECEPTOR BETA-3R; 1.
112
+ DR Pfam; PF00001; 7tm_1; 1.
113
+ DR PRINTS; PR00513; 5HT1BRECEPTR.
114
+ DR PRINTS; PR01101; 5HTRECEPTOR.
115
+ DR PRINTS; PR00237; GPCRRHODOPSN.
116
+ DR SMART; SM01381; 7TM_GPCR_Srsx; 1.
117
+ DR SUPFAM; SSF81321; Family A G protein-coupled receptor-like; 1.
118
+ DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1.
119
+ DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1.
120
+ PE 2: Evidence at transcript level;
121
+ KW Behavior; Cell membrane; Disulfide bond; G-protein coupled receptor;
122
+ KW Glycoprotein; Lipoprotein; Membrane; Palmitate; Phosphoprotein; Receptor;
123
+ KW Reference proteome; Transducer; Transmembrane; Transmembrane helix.
124
+ FT CHAIN 1..390
125
+ FT /note="5-hydroxytryptamine receptor 1B"
126
+ FT /id="PRO_0000068920"
127
+ FT TOPO_DOM 1..49
128
+ FT /note="Extracellular"
129
+ FT /evidence="ECO:0000250"
130
+ FT TRANSMEM 50..75
131
+ FT /note="Helical; Name=1"
132
+ FT /evidence="ECO:0000250"
133
+ FT TOPO_DOM 76..84
134
+ FT /note="Cytoplasmic"
135
+ FT /evidence="ECO:0000250"
136
+ FT TRANSMEM 85..110
137
+ FT /note="Helical; Name=2"
138
+ FT /evidence="ECO:0000250"
139
+ FT TOPO_DOM 111..123
140
+ FT /note="Extracellular"
141
+ FT /evidence="ECO:0000250"
142
+ FT TRANSMEM 124..145
143
+ FT /note="Helical; Name=3"
144
+ FT /evidence="ECO:0000250"
145
+ FT TOPO_DOM 146..165
146
+ FT /note="Cytoplasmic"
147
+ FT /evidence="ECO:0000250"
148
+ FT TRANSMEM 166..187
149
+ FT /note="Helical; Name=4"
150
+ FT /evidence="ECO:0000250"
151
+ FT TOPO_DOM 188..205
152
+ FT /note="Extracellular"
153
+ FT /evidence="ECO:0000250"
154
+ FT TRANSMEM 206..228
155
+ FT /note="Helical; Name=5"
156
+ FT /evidence="ECO:0000250"
157
+ FT TOPO_DOM 229..315
158
+ FT /note="Cytoplasmic"
159
+ FT /evidence="ECO:0000250"
160
+ FT TRANSMEM 316..336
161
+ FT /note="Helical; Name=6"
162
+ FT /evidence="ECO:0000250"
163
+ FT TOPO_DOM 337..349
164
+ FT /note="Extracellular"
165
+ FT /evidence="ECO:0000250"
166
+ FT TRANSMEM 350..371
167
+ FT /note="Helical; Name=7"
168
+ FT /evidence="ECO:0000250"
169
+ FT TOPO_DOM 372..390
170
+ FT /note="Cytoplasmic"
171
+ FT /evidence="ECO:0000250"
172
+ FT REGION 260..282
173
+ FT /note="Disordered"
174
+ FT /evidence="ECO:0000256|SAM:MobiDB-lite"
175
+ FT MOTIF 146..148
176
+ FT /note="DRY motif; important for ligand-induced conformation
177
+ FT changes and signaling"
178
+ FT /evidence="ECO:0000250"
179
+ FT MOTIF 365..369
180
+ FT /note="NPxxY motif; important for ligand-induced
181
+ FT conformation changes and signaling"
182
+ FT /evidence="ECO:0000250"
183
+ FT BINDING 129
184
+ FT /ligand="ergotamine"
185
+ FT /ligand_id="ChEBI:CHEBI:190463"
186
+ FT /ligand_note="agonist"
187
+ FT /evidence="ECO:0000250|UniProtKB:P28222"
188
+ FT BINDING 134
189
+ FT /ligand="ergotamine"
190
+ FT /ligand_id="ChEBI:CHEBI:190463"
191
+ FT /ligand_note="agonist"
192
+ FT /evidence="ECO:0000250|UniProtKB:P28222"
193
+ FT BINDING 201
194
+ FT /ligand="ergotamine"
195
+ FT /ligand_id="ChEBI:CHEBI:190463"
196
+ FT /ligand_note="agonist"
197
+ FT /evidence="ECO:0000250|UniProtKB:P28222"
198
+ FT SITE 355
199
+ FT /note="Important for species-specific agonist sensitivity"
200
+ FT /evidence="ECO:0000250"
201
+ FT LIPID 388
202
+ FT /note="S-palmitoyl cysteine"
203
+ FT /evidence="ECO:0000255"
204
+ FT CARBOHYD 24
205
+ FT /note="N-linked (GlcNAc...) asparagine"
206
+ FT /evidence="ECO:0000255"
207
+ FT CARBOHYD 32
208
+ FT /note="N-linked (GlcNAc...) asparagine"
209
+ FT /evidence="ECO:0000255"
210
+ FT DISULFID 122..199
211
+ FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00521"
212
+ FT CONFLICT 5
213
+ FT /note="G -> S (in Ref. 1 and 3)"
214
+ FT /evidence="ECO:0000305"
215
+ FT CONFLICT 7
216
+ FT /note="Q -> R (in Ref. 1 and 3)"
217
+ FT /evidence="ECO:0000305"
218
+ FT CONFLICT 14
219
+ FT /note="Missing (in Ref. 1 and 3)"
220
+ FT /evidence="ECO:0000305"
221
+ FT CONFLICT 171
222
+ FT /note="R -> A (in Ref. 1 and 3)"
223
+ FT /evidence="ECO:0000305"
224
+ SQ SEQUENCE 390 AA; 43496 MW; C22EBC077C6C897D CRC64;
225
+ MEEPGAQCAP PLAAGSQIAV PQANLSAAHS HNCSAEGYIY QDSIALPWKV LLVLLLALFT
226
+ LATTLSNAFV VATVYRTRKL HTPANYLIAS LAVTDLLVSI LVMPISTMYT VTGRWTLGQV
227
+ VCDLWLSSDI TCCTASIMHL CVIALDRYWA ITDAVEYSAK RTPKRAAIMI RLVWVFSICI
228
+ SLPPFFWRQA KAEEEVSECL VNTDHVLYTV YSTVGAFYLP TLLLIALYGR IYVEARSRIL
229
+ KQTPNRTGKR LTRAQLITDS PGSTTSVTSI NSRAPDVPSE SGSPVYVNQV KVRVSDALLE
230
+ KKKLMAARER KATKTLGIIL GVFIVCWLPF FIISLVMPIC KDACWFHQAI FDFFTWLGYV
231
+ NSLINPIIYT MSNEDFKQAF HKLIRFKCTS
232
+ //
data/test/functional/bio/test_command.rb CHANGED
@@ -187,8 +187,10 @@ module Bio
187
187
  return
188
188
  end
189
189
  assert_equal('', str.to_s.strip)
190
+ assert_equal('', err.to_s.strip)
190
191
  str, err = Bio::Command.query_command_open3(ary, @data)
191
192
  assert_equal(@sorted, str.to_s.strip.split(/\s+/))
193
+ assert_equal('', err.to_s.strip)
192
194
  end
193
195
  end #class FuncTestCommandQuery
194
196
 
data/test/network/bio/db/kegg/test_genes_hsa7422.rb CHANGED
@@ -38,7 +38,8 @@ module Bio
38
38
  "H01457 Diabetic retinopathy",
39
39
  "H01459 Diabetic neuropathy",
40
40
  "H01529 Avascular necrosis of femoral head",
41
- "H01709 Glucocorticoid-induced osteonecrosis"]
41
+ "H01709 Glucocorticoid-induced osteonecrosis",
42
+ "H02559 Microvascular complications of diabetes"]
42
43
 
43
44
  assert_equal(expected, @obj.diseases_as_strings)
44
45
  end
@@ -48,41 +49,54 @@ module Bio
48
49
  "H01457"=>"Diabetic retinopathy",
49
50
  "H01459"=>"Diabetic neuropathy",
50
51
  "H01529"=>"Avascular necrosis of femoral head",
51
- "H01709"=>"Glucocorticoid-induced osteonecrosis"}
52
+ "H01709"=>"Glucocorticoid-induced osteonecrosis",
53
+ "H02559"=>"Microvascular complications of diabetes"}
52
54
  assert_equal(expected, @obj.diseases_as_hash)
53
55
  end
54
56
 
55
57
  def test_drug_targets_as_strings
56
58
  expected = ["Abicipar pegol: D11517",
57
- "Aflibercept: D09574",
58
- "Aflibercept beta: D10819",
59
- "Bevacizumab: D06409",
59
+ "Aflibercept: D09574<JP/US>",
60
+ "Aflibercept beta: D10819<JP>",
61
+ "Bevacizumab: D06409<JP/US>",
60
62
  "Bevasiranib sodium: D08874",
61
- "Brolucizumab: D11083",
62
- "Faricimab: D11516",
63
+ "Brolucizumab: D11083<JP/US>",
64
+ "Dilpacimab: D11642",
65
+ "Emvododstat: D11890",
66
+ "Faricimab: D11516<JP/US>",
63
67
  "Navicixizumab: D11126",
64
68
  "Pegaptanib: D05386",
65
- "Ranibizumab: D05697",
69
+ "Ranibizumab: D05697<JP/US>",
70
+ "Tarcocimab: D12507",
71
+ "Tarcocimab tedromer: D12508",
66
72
  "Vanucizumab: D11244"]
67
73
  assert_equal(expected, @obj.drug_targets_as_strings)
68
74
  end
69
75
 
70
76
  def test_networks_as_strings
71
- expected = ["nt06114 PI3K signaling (virus)",
72
- "nt06124 Chemokine signaling (virus)",
77
+ expected = ["nt06124 Chemokine signaling (viruses)",
73
78
  "nt06164 Kaposi sarcoma-associated herpesvirus (KSHV)",
74
- "nt06214 PI3K signaling",
75
79
  "nt06219 JAK-STAT signaling",
76
80
  "nt06224 CXCR signaling",
77
81
  "nt06225 HIF-1 signaling",
82
+ "nt06227 Nuclear receptor signaling",
78
83
  "nt06262 Pancreatic cancer",
79
84
  "nt06264 Renal cell carcinoma",
85
+ "nt06360 Cushing syndrome",
86
+ "nt06526 MAPK signaling",
87
+ "nt06528 Calcium signaling",
88
+ "nt06530 PI3K signaling",
80
89
  "N00079 HIF-1 signaling pathway",
81
90
  "N00080 Loss of VHL to HIF-1 signaling pathway",
82
91
  "N00081 Mutation-inactivated VHL to HIF-1 signaling pathway",
83
92
  "N00095 ERBB2-overexpression to EGF-Jak-STAT signaling pathway",
84
93
  "N00157 KSHV vGPCR to GNB/G-ERK signaling pathway",
85
- "N00179 KSHV K1 to PI3K-NFKB signaling pathway"]
94
+ "N00317 AhR signaling pathway",
95
+ "N01412 Metals to HTF-1 signaling pathway",
96
+ "N01592 GF-RTK-RAS-ERK signaling pathway",
97
+ "N01641 RTK-PLCG-ITPR signaling pathway",
98
+ "N01656 GF-RTK-PI3K signaling pathway",
99
+ "N01658 GF-RTK-RAS-PI3K signaling pathway"]
86
100
  assert_equal(expected, @obj.networks_as_strings)
87
101
  end
88
102