Most of the services provided with the Phenoscape Knowledgebase (KB) API return data in JSON format, plain text (usually tab-delimited), and NeXML. This package facilitates interfacing with the Phenoscape Knowledgebase for searching ontology terms, retrieving term info, and querying data matrices.
The development version of RPhenoscape is available on Github. It has
not yet been released to [CRAN]. To install RPhenoscape from Github, use
the install_github() function in the remotes
package (which can be installed from CRAN using
install.packages()). See the package README for
details.
Once installed, the package can be loaded (“attached”) as any other R package:
Use OntoTrace to obtain a character matrix of inferred and author-asserted presence/absence associations for a taxonomic clade and anatomical region of interest.
The ontotrace
endpoint in the Phenoscape KB API returns the presence/absence
character matrix in NeXML format. The first step is to get the NeXML
object using get_ontotrace_data method.
nex <- get_ontotrace_data(taxon = c("Ictalurus", "Ameiurus"), entity = "fin spine")The result is an object of class nexml defined in the
RNeXML package. The object mirrors the structure of a NeXML file, and
can be inspected accordingly. Note that although generically NeXML files
can contain multiple OTUs blocks and multiple characters blocks, NeXML
files generated by the KB’s OntoTrace API contain only one. This means
we can, for example, inspect the number of taxa and characters as
follows:
# number of taxa in the first (and only) OTUs block
length(nex@otus[[1]]@otu)[1] 15
# number of characters in the first (and only) characters block
length(nex@characters[[1]]@format@char)[1] 2More details on the nexml
object can be found in the RNeXML documentation.
Then retrieve wanted information from the NeXML object.
Get character matrix:
(m <- get_char_matrix(nex)) taxa otu otus
1 Ameiurus brunneus VTO_0036273 tcb028860-571e-478a-9449-947a521946a1
2 Ameiurus catus VTO_0036275 tcb028860-571e-478a-9449-947a521946a1
3 Ameiurus melas VTO_0036272 tcb028860-571e-478a-9449-947a521946a1
4 Ameiurus natalis VTO_0036274 tcb028860-571e-478a-9449-947a521946a1
5 Ameiurus nebulosus VTO_0036278 tcb028860-571e-478a-9449-947a521946a1
6 Ameiurus platycephalus VTO_0036276 tcb028860-571e-478a-9449-947a521946a1
7 Ameiurus serracanthus VTO_0036277 tcb028860-571e-478a-9449-947a521946a1
8 Ictalurus australis VTO_0061495 tcb028860-571e-478a-9449-947a521946a1
9 Ictalurus balsanus VTO_0036221 tcb028860-571e-478a-9449-947a521946a1
10 Ictalurus dugesii VTO_0061497 tcb028860-571e-478a-9449-947a521946a1
11 Ictalurus furcatus VTO_0036223 tcb028860-571e-478a-9449-947a521946a1
12 Ictalurus lupus VTO_0036220 tcb028860-571e-478a-9449-947a521946a1
13 Ictalurus mexicanus VTO_0061498 tcb028860-571e-478a-9449-947a521946a1
14 Ictalurus pricei VTO_0036218 tcb028860-571e-478a-9449-947a521946a1
15 Ictalurus punctatus VTO_0036225 tcb028860-571e-478a-9449-947a521946a1
anterior dentation of pectoral fin spine
1 1
2 1
3 NA
4 NA
5 1
6 1
7 1
8 1
9 0
10 NA
11 0
12 1
13 NA
14 1
15 1
anterior distal serration of pectoral fin spine
1 1
2 1
3 0 and 1
4 1
5 1
6 1
7 1
8 1
9 0 and 1
10 1
11 1
12 1
13 1
14 1
15 1The character matrix can be integrated with other data, such as meta data which include taxon identifiers, character identifiers, etc. Get meta data:
(meta <- get_char_matrix_meta(nex))$id_taxa
label href
1 Ameiurus catus http://purl.obolibrary.org/obo/VTO_0036275
2 Ictalurus pricei http://purl.obolibrary.org/obo/VTO_0036218
3 Ictalurus punctatus http://purl.obolibrary.org/obo/VTO_0036225
4 Ameiurus serracanthus http://purl.obolibrary.org/obo/VTO_0036277
5 Ameiurus natalis http://purl.obolibrary.org/obo/VTO_0036274
6 Ictalurus furcatus http://purl.obolibrary.org/obo/VTO_0036223
7 Ameiurus brunneus http://purl.obolibrary.org/obo/VTO_0036273
8 Ictalurus balsanus http://purl.obolibrary.org/obo/VTO_0036221
9 Ictalurus mexicanus http://purl.obolibrary.org/obo/VTO_0061498
10 Ictalurus lupus http://purl.obolibrary.org/obo/VTO_0036220
11 Ameiurus platycephalus http://purl.obolibrary.org/obo/VTO_0036276
12 Ameiurus nebulosus http://purl.obolibrary.org/obo/VTO_0036278
13 Ictalurus australis http://purl.obolibrary.org/obo/VTO_0061495
14 Ameiurus melas http://purl.obolibrary.org/obo/VTO_0036272
15 Ictalurus dugesii http://purl.obolibrary.org/obo/VTO_0061497
otu otus
1 VTO_0036275 tcb028860-571e-478a-9449-947a521946a1
2 VTO_0036218 tcb028860-571e-478a-9449-947a521946a1
3 VTO_0036225 tcb028860-571e-478a-9449-947a521946a1
4 VTO_0036277 tcb028860-571e-478a-9449-947a521946a1
5 VTO_0036274 tcb028860-571e-478a-9449-947a521946a1
6 VTO_0036223 tcb028860-571e-478a-9449-947a521946a1
7 VTO_0036273 tcb028860-571e-478a-9449-947a521946a1
8 VTO_0036221 tcb028860-571e-478a-9449-947a521946a1
9 VTO_0061498 tcb028860-571e-478a-9449-947a521946a1
10 VTO_0036220 tcb028860-571e-478a-9449-947a521946a1
11 VTO_0036276 tcb028860-571e-478a-9449-947a521946a1
12 VTO_0036278 tcb028860-571e-478a-9449-947a521946a1
13 VTO_0061495 tcb028860-571e-478a-9449-947a521946a1
14 VTO_0036272 tcb028860-571e-478a-9449-947a521946a1
15 VTO_0061497 tcb028860-571e-478a-9449-947a521946a1
$id_entities
label
1 anterior dentation of pectoral fin spine
2 anterior distal serration of pectoral fin spine
href char
1 http://purl.obolibrary.org/obo/UBERON_2002001 UBERON_2002001
2 http://purl.obolibrary.org/obo/UBERON_2002002 UBERON_2002002To obtain the character matrices for studies published for a taxonomic clade and anatomical region of interest.
First step is to retrieve the list of studies given a taxonomic clade
and anatomical structures (returned as data.frame).
(slist <- get_studies(taxon = "Ictalurus australis", entity = "fin")) id
1 https://scholar.google.com/scholar?q=The+Phylogeny+of+Ictalurid+Catfishes%3A+A+Synthesis+of+Recent+Work&btnG=&hl=en&as_sdt=0%2C42
label
1 Lundberg (1992)Based off the study ids retained from previous step, get the
evolutionary character matrix for each study id (in NeXML-format) using
get_study_data.
(nex_list <- get_study_data(slist$id))$`https://scholar.google.com/scholar?q=The+Phylogeny+of+Ictalurid+Catfishes%3A+A+Synthesis+of+Recent+Work&btnG=&hl=en&as_sdt=0%2C42`
A nexml object representing:
0 phylogenetic tree block(s),
1 character block(s), where:
block 1 defines 115 standard/discrete character(s), with 2 to 7 states
and 0 polymorphic or uncertain state(s) defined
matrix 1 has 22 row(s)
22 taxonomic units in 1 block(s)
Taxa: Noturus flavus, Ictalurus lupus, Noturus insignis, Ameiurus nebulosus, Ictalurus pricei, Pylodictis olivaris ...
Metadata annotations:
3 at top level
22 in block 1 at otu level
115 in block 1 at char level
734 in block 1 at state level
NeXML generated by RNeXML using schema version: 0.9
Size: 7.3 Mb From the list of NeXML objects, retrieve the character matrices.
study_matrix <- lapply(nex_list, function(nex) get_char_matrix(nex, otus_id = FALSE, states_as_labels = TRUE))
study_matrix[[1]][1:5, 1:5] taxa otu
1 Ameiurus brunneus otu_331eacec-f62a-489b-aa97-01f88c469d4a
2 Ameiurus catus otu_f0b4abb4-c4ca-4d99-b6d3-d069176eea82
3 Ameiurus melas otu_5a3062f1-9803-4120-ae34-d2aa1ce02a75
4 Ameiurus natalis otu_b92dfa0d-8c16-4228-815f-c418c6e92781
5 Ameiurus nebulosus otu_31f42c8a-cd70-4bf4-994d-9bc483822ba7
Anal-fin rays, species mean count Anterior dentations of pectoral spine
1 16.1-20 large
2 20.1-25.5 moderate
3 20.1-25.5 small
4 25.6-28 small
5 20.1-25.5 moderate
Anterior distal serrae of pectoral spine
1 <3 moderately sharp serrae
2 3-6 moderately sharp serrae
3 absent or scarcely developed
4 3-6 moderately sharp serrae
5 <3 moderately sharp serraeEach character matrix can be integrated with other data, such as meta data which include taxon identifiers, character identifiers, etc. Get meta data:
study_metas <- lapply(nex_list, function(nex) get_char_matrix_meta(nex))
study_metas[[1]]$id_taxa
label href
1 Noturus flavus http://purl.obolibrary.org/obo/VTO_0036263
2 Ictalurus lupus http://purl.obolibrary.org/obo/VTO_0036220
3 Noturus insignis http://purl.obolibrary.org/obo/VTO_0036237
4 Ameiurus nebulosus http://purl.obolibrary.org/obo/VTO_0036278
5 Ictalurus pricei http://purl.obolibrary.org/obo/VTO_0036218
6 Pylodictis olivaris http://purl.obolibrary.org/obo/VTO_0036282
7 Ameiurus melas http://purl.obolibrary.org/obo/VTO_0036272
8 Prietella phreatophila http://purl.obolibrary.org/obo/VTO_0036265
9 Ameiurus natalis http://purl.obolibrary.org/obo/VTO_0036274
10 Ictalurus australis http://purl.obolibrary.org/obo/VTO_0061495
11 Ameiurus catus http://purl.obolibrary.org/obo/VTO_0036275
12 Ameiurus brunneus http://purl.obolibrary.org/obo/VTO_0036273
13 Ictalurus furcatus http://purl.obolibrary.org/obo/VTO_0036223
14 Noturus stigmosus http://purl.obolibrary.org/obo/VTO_0036261
15 Ameiurus serracanthus http://purl.obolibrary.org/obo/VTO_0036277
16 Ictalurus mexicanus http://purl.obolibrary.org/obo/VTO_0061498
17 Satan eurystomus http://purl.obolibrary.org/obo/VTO_0061485
18 Ictalurus dugesii http://purl.obolibrary.org/obo/VTO_0061497
19 Trogloglanis pattersoni http://purl.obolibrary.org/obo/VTO_0061501
20 Ameiurus platycephalus http://purl.obolibrary.org/obo/VTO_0036276
21 Ictalurus balsanus http://purl.obolibrary.org/obo/VTO_0036221
22 Ictalurus punctatus http://purl.obolibrary.org/obo/VTO_0036225
otu
1 otu_3d644586-19a2-49d5-ab3c-673f483c362f
2 otu_7359fcc3-edb3-4ed9-a236-c1e846b8a5f6
3 otu_dddcc44c-8c9a-40a7-a7b3-277ce9871593
4 otu_31f42c8a-cd70-4bf4-994d-9bc483822ba7
5 otu_da138745-cedf-4cbc-8305-0e602518548c
6 otu_f2bb7423-f928-4655-a602-5c2143f1c877
7 otu_5a3062f1-9803-4120-ae34-d2aa1ce02a75
8 otu_40ea9c47-775f-4be1-80da-c4b7535ad5ce
9 otu_b92dfa0d-8c16-4228-815f-c418c6e92781
10 otu_01d184a9-d779-42dd-b6bc-1764b04d4cb1
11 otu_f0b4abb4-c4ca-4d99-b6d3-d069176eea82
12 otu_331eacec-f62a-489b-aa97-01f88c469d4a
13 otu_8257dd55-8ed2-409f-b92a-cb9e609da7cb
14 otu_b2b0135f-ded2-4f4b-8e4e-1d015ad342e2
15 otu_6eff3beb-3ab5-4b2c-a104-4a5821fbb152
16 otu_3dde3e49-d73d-48bb-945b-fc97f2040cc0
17 otu_eeefeec8-36f7-4b66-9002-ca445fce493c
18 otu_0b52014d-f9df-4cc3-9694-48c0234c195b
19 otu_b42e7ffd-330e-4ea2-a099-fb59a0058857
20 otu_aa535d43-f38d-435e-b7d5-3f413e7ad714
21 otu_2b0b6c19-e51c-400f-b738-000d9d82a36f
22 otu_0ac943f8-08df-4b21-ba82-cea20cff25cd
otus
1 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
2 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
3 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
4 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
5 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
6 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
7 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
8 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
9 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
10 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
11 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
12 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
13 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
14 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
15 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
16 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
17 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
18 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
19 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
20 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
21 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
22 otus_623e5db5-d4a5-40b9-b087-e4047cea0e75
$id_entities
label
1 Posterior flap of adipose fin
2 Gill membranes
3 Orbital rim
4 Caudal fin
5 Lateral line extent
6 Mesethmoid cornua
7 Width of snout across mesethmoid cornua
8 Width of mesethmoid neck
9 Cross-sectional form of skull (juveniles and young adults)
10 Neurocranial width at epiphyseal bar
11 Posterior cranial fontanelle (adults)
12 Supraoccipital process and associated supraneural
13 Sagittal crests on skull roof
14 Transverse occipital crests
15 Muscle crests on margin of frontal
16 Sculpturing pattern of supraoccipital crests
17 Anterior extent of sphenotic
18 Sphenotic process
19 Extrascapular bone composition
20 Pterotic wing shape
21 Pterotic surface
22 Nasal shape
23 Infraorbital bones
24 Lateral ethmoid wing
25 Superficial ophthalmic nerve foramen
26 Orbital foramen
27 Parasphenoid stem
28 Ascending wings of parasphenoid
29 Posterior end of adductor arcus palatini scar on parasphenoid
30 Vertical wing of frontal
31 Pterosphenoid-prootic joint
32 Orbitosphenoid shelves
33 Prootic-exoccipital joint
34 Prootic-basioccipital joint
35 Optic foramen
36 Mandible length
37 Mandibular sensory canal pores, species modes
38 First mandibular sensory pore and tube
39 Mandibular symphyseal ventral process
40 Anteroventral crest of dentary
41 Coronoid process
42 Posterior process of articular
43 Premaxilla width
44 Mesial process of premaxilla
45 Lateral process of premaxilla
46 Premaxillary teeth-size and number
47 Jaw teeth-shape and size gradation
48 Jaw adductor musculature-A3 layer
49 Palatine length
50 Hyomandibular (otic region joint) shape
51 Anterior process of hyomandibular
52 Opercular facet position on posterior edge of hyomandibular
53 Hyomandibular-metapterygoid joint
54 Hyomandibular-quadrate joint
55 Scar on hyomandibular for A3 bundle of jaw adductor musculature
56 Crest on hyomandibular for levator arcus palatini muscle
57 Crest on hyomandibular for A2 bundle of jaw adductor muscle
58 Crest on hyomandibular for levator operculi muscle
59 Process on hyomandibular for adductor hyomandibularis muscle
60 External foramen of facial nerve canal through hyomandibular
61 Symplectic canal
62 Jaw adductor muscle attachment surface on preopercle
63 Upper limb of preopercle
64 Suprapreopercle
65 Quadrate-metapterygoid joint length
66 Quadrate-metapterygoid joint composition
67 Metapterygoid form
68 Endopterygoid size
69 Epihyal-ceratohyal joint
70 Dorsal edge of ceratohyal
71 Epihyal shape
72 Ceratohyal-ventral hypohyal joint
73 Dorsal hypohyal
74 Urohyal shape
75 Opercle shape
76 Scar on opercle for levator operculi muscle
77 Interopercle shape
78 Dorsal pits on first centrum
79 Ventral ridges on first centrum
80 Development of superficial ossification
81 Anterior limb of fourth transverse process
82 Vertical lamina between third and fourth neural spines
83 Neural complex = supraneural 3
84 Depth of Weberian complex
85 Gas bladder
86 Precaudal vertebrae, species mean number
87 Caudal vertebrae, species mean number
88 Hypurals
89 Hypurapophysis
90 Caudal-fin branched ray numbers
91 Middle Nuchal plate of first dorsal-fin pterygiophore
92 Spine base condyles on second dorsal-fin pterygiophore
93 Dorsal-fin spine development
94 Anal-fin rays, species mean count
95 Pectoral-fin soft rays, species modal count
96 Pectoral-fin radials
97 Ornamentation pattern on posterior cleithral process
98 Length of posterior cleithral process
99 Length of cleithral symphysis
100 Coracoid midline sutures, species mean count
101 Ventral keel of coracoid
102 Secondary keel on coracoid below scapular foramen
103 Extensor muscle fossa on coracoid
104 Transcapular ligament
105 Subpterotic process of supracleithrum
106 Pectoral spine tip
107 Anterior distal serrae of pectoral spine
108 Anterior dentations of pectoral spine
109 Anterior ridge of pectoral spine
110 Posterior dentation shape
111 Posterior dentation bases
112 Pectoral spine late ontogeny
113 Posterolateral process of basipterygium
114 Pelvic splint
115 Pelvic-fin rays, species modal counts
href
1 http://purl.org/phenoscape/uuid/9a83ecb3-e4fc-4232-8144-c90dd8c9f19b
2 http://purl.org/phenoscape/uuid/1c9fac46-3ea1-414a-a43b-18a8cbc94371
3 http://purl.org/phenoscape/uuid/9484e795-2f20-459c-9fc0-75118931d621
4 http://purl.org/phenoscape/uuid/89a17565-fb95-4d57-9db6-654724adb470
5 http://purl.org/phenoscape/uuid/9480950e-79ae-4c8e-98f3-4e55663ecf8f
6 http://purl.org/phenoscape/uuid/22489031-7e11-4ccf-98bf-45f2f7d3cce5
7 http://purl.org/phenoscape/uuid/95b0a238-5fe4-43ce-add4-170435e42f97
8 http://purl.org/phenoscape/uuid/227408ae-0263-4807-87ab-87a54e7c50eb
9 http://purl.org/phenoscape/uuid/ac1a1cf3-e53f-4ff3-942c-6efd2f549475
10 http://purl.org/phenoscape/uuid/803947a1-c916-4bc4-9caf-c778c13b22e7
11 http://purl.org/phenoscape/uuid/3742927c-cc89-48e3-aa98-172dc002f370
12 http://purl.org/phenoscape/uuid/d26f34da-4b90-489f-85e7-9d590fbbceae
13 http://purl.org/phenoscape/uuid/8c76a977-8157-4554-ac76-b28a4a2ff755
14 http://purl.org/phenoscape/uuid/3fe604f9-526d-4c37-aac8-5ebf1888a1b5
15 http://purl.org/phenoscape/uuid/05ed62ee-3bad-4c76-93c1-6e0a70507d7e
16 http://purl.org/phenoscape/uuid/76876861-2e77-4337-9a45-f44417d60595
17 http://purl.org/phenoscape/uuid/83588dd3-18ac-4784-ad19-57f48ef5af8d
18 http://purl.org/phenoscape/uuid/ae7b7c50-3783-4a2e-b933-45e880dc7a1a
19 http://purl.org/phenoscape/uuid/0280336a-d748-4c84-8296-ebf9881c299a
20 http://purl.org/phenoscape/uuid/0fd57ff4-627f-49ea-b421-7f93c2147a18
21 http://purl.org/phenoscape/uuid/87a31a84-3413-4a85-a009-911f51015a98
22 http://purl.org/phenoscape/uuid/39b4b20f-2bd3-4ace-9907-fa531478bb76
23 http://purl.org/phenoscape/uuid/b65c0d5a-d63d-4283-bf51-78d1af8bfe70
24 http://purl.org/phenoscape/uuid/b0d1b8af-17ec-4c4e-82c6-39a4eedc1938
25 http://purl.org/phenoscape/uuid/a16aee1f-6463-4a7c-8770-7fdca8ec82e8
26 http://purl.org/phenoscape/uuid/d8365a53-7640-4dca-bc2c-cafc56864474
27 http://purl.org/phenoscape/uuid/da3aa64a-5613-473e-a561-f96c2ae85990
28 http://purl.org/phenoscape/uuid/b2affab0-6157-419a-aaa0-f3bb5f696ad9
29 http://purl.org/phenoscape/uuid/95113a49-6854-484b-8152-4a9e0265a0e9
30 http://purl.org/phenoscape/uuid/e1f6a2fa-77d7-48d1-ae71-920b6c7088dc
31 http://purl.org/phenoscape/uuid/3d2cb310-9a25-457e-a5c7-637cb00e6be3
32 http://purl.org/phenoscape/uuid/b8b91632-9f40-4b3f-ae77-7923008ebdb7
33 http://purl.org/phenoscape/uuid/f2bd54a8-a819-41eb-9b62-ceeeaa72ae21
34 http://purl.org/phenoscape/uuid/ae8b895b-7b5e-475c-a3d7-91de3c2f32b7
35 http://purl.org/phenoscape/uuid/788ac46f-a7fa-4bb9-99b8-bbbc605ef9f6
36 http://purl.org/phenoscape/uuid/1a13d23b-88f6-4b66-8fce-2fbdcaae8ca0
37 http://purl.org/phenoscape/uuid/39eff64e-06dc-45e3-92af-b10f3afca103
38 http://purl.org/phenoscape/uuid/4648c2dd-206a-43fe-8174-cd681f9ce979
39 http://purl.org/phenoscape/uuid/a68adcb1-4fe6-4092-9d77-cb823e08b247
40 http://purl.org/phenoscape/uuid/febb5d18-e38b-4b86-ada0-91039afb411c
41 http://purl.org/phenoscape/uuid/f9024429-23a1-4681-bcaf-a684756c5658
42 http://purl.org/phenoscape/uuid/859c0edc-66f4-4bee-8342-e9f0999ed052
43 http://purl.org/phenoscape/uuid/c175f441-7aa8-4387-90c7-7c62c97d1143
44 http://purl.org/phenoscape/uuid/ec73df3f-d73e-48f4-b670-db4fdbff3c6b
45 http://purl.org/phenoscape/uuid/5305450f-86e2-4d15-8e91-c239fb4763e5
46 http://purl.org/phenoscape/uuid/28478ece-5f6d-4ed6-a93e-5b21475e9594
47 http://purl.org/phenoscape/uuid/ae2ba00b-b732-4ec0-8cc5-13736e98ebbe
48 http://purl.org/phenoscape/uuid/f581c9a1-851a-4628-9eff-bd32f4c096e5
49 http://purl.org/phenoscape/uuid/99b89fad-dd49-49ec-9ad3-a21c3e150565
50 http://purl.org/phenoscape/uuid/580367a2-4824-4745-823d-9ba5a91fb2b9
51 http://purl.org/phenoscape/uuid/6af3a531-b5d1-40ff-87a6-aa9ade63e718
52 http://purl.org/phenoscape/uuid/9c84117e-dd73-4293-b2bc-fd7acf109452
53 http://purl.org/phenoscape/uuid/090617eb-c026-44b0-a75e-44407f2082c8
54 http://purl.org/phenoscape/uuid/eb3d5418-19de-4dcb-93f3-8a5c4d83c172
55 http://purl.org/phenoscape/uuid/54778867-6f82-4af6-b7c1-343d35bbbba2
56 http://purl.org/phenoscape/uuid/48ac528c-dc6c-451a-8d65-7031ae2bd066
57 http://purl.org/phenoscape/uuid/3963090a-c1e9-4ccc-9396-968b6f30a017
58 http://purl.org/phenoscape/uuid/c9d79125-f471-484a-9511-2ec53f5072bf
59 http://purl.org/phenoscape/uuid/e85e3e47-04cc-4d65-95f3-3fdb9323ce96
60 http://purl.org/phenoscape/uuid/1e720a22-afac-4303-b2b7-7efa8970c141
61 http://purl.org/phenoscape/uuid/31ff5ea8-d2eb-4c60-8ac8-6851ca5843d4
62 http://purl.org/phenoscape/uuid/10d3e995-8a01-4751-bbfd-880b56833a27
63 http://purl.org/phenoscape/uuid/80812d32-14c5-4027-9653-f3d3ded9a784
64 http://purl.org/phenoscape/uuid/07eaad99-30e6-4595-b4ab-a6bc3bef5658
65 http://purl.org/phenoscape/uuid/be43fee2-d0ab-4f39-985c-b49d1ea479aa
66 http://purl.org/phenoscape/uuid/05fa3ccb-2ce4-4b4b-b48e-143d356d7c98
67 http://purl.org/phenoscape/uuid/8dd70efe-4599-49db-9054-bbb1c0692cf8
68 http://purl.org/phenoscape/uuid/9c863f1f-f590-4e5b-bd0a-484e0138a50e
69 http://purl.org/phenoscape/uuid/30194856-8c2d-42b1-b517-42706ea0030e
70 http://purl.org/phenoscape/uuid/ddd00db5-1cc7-4e0f-bee1-9537df0b265c
71 http://purl.org/phenoscape/uuid/ca4896f6-aa02-4ab7-b362-642e989583fd
72 http://purl.org/phenoscape/uuid/e2cfb2f5-d39f-4a4c-99fc-aefd3fda6813
73 http://purl.org/phenoscape/uuid/48d0bc1b-69fc-4ce6-a879-2e9962c70626
74 http://purl.org/phenoscape/uuid/6fd3f3e8-2351-4355-90bf-3c8d2dba499d
75 http://purl.org/phenoscape/uuid/de8f4c54-c823-4148-978e-d0a80fb4386e
76 http://purl.org/phenoscape/uuid/5b5c781b-67b7-4081-bcaf-cebf1595c547
77 http://purl.org/phenoscape/uuid/5dc41c8b-4a39-4c79-8d3f-06a5e37157f1
78 http://purl.org/phenoscape/uuid/001feaf3-b8b5-4f33-9358-b3969c76b7e2
79 http://purl.org/phenoscape/uuid/230958be-876d-4b3c-af7f-e79fd4bf857a
80 http://purl.org/phenoscape/uuid/a87a010c-8078-41a6-acbf-204dbce551e6
81 http://purl.org/phenoscape/uuid/b1787273-01a1-4203-8661-695b8564eeb4
82 http://purl.org/phenoscape/uuid/b8ab17e1-e3eb-4372-84e6-2b49c7f94da8
83 http://purl.org/phenoscape/uuid/3fe42c23-8fbd-4371-9d86-c2ca24b990d8
84 http://purl.org/phenoscape/uuid/1eaee821-8bb7-4194-b711-e598c546ab3e
85 http://purl.org/phenoscape/uuid/266987fb-17cc-464f-9806-372dc7c8ce4b
86 http://purl.org/phenoscape/uuid/6d8fceb6-d688-4d44-9607-39a71b94cd6d
87 http://purl.org/phenoscape/uuid/eadf2a00-723e-425a-b226-78dab22a67de
88 http://purl.org/phenoscape/uuid/64f47595-dcf1-4b9c-aadf-2822545c63d7
89 http://purl.org/phenoscape/uuid/0a85e808-e9e7-4466-bbc4-72e24ec80ca2
90 http://purl.org/phenoscape/uuid/065964c2-7eeb-45c5-9cef-35d717c83ba0
91 http://purl.org/phenoscape/uuid/941de864-9689-4e4c-8b7b-fcb1be051247
92 http://purl.org/phenoscape/uuid/3e8489ee-eae2-429b-9613-dc1f9086ff9a
93 http://purl.org/phenoscape/uuid/22ae7b38-a1d3-4859-8950-95dc94eaaa47
94 http://purl.org/phenoscape/uuid/9c935a10-8744-4a6e-af5f-6c9851158877
95 http://purl.org/phenoscape/uuid/5bab9b4c-0da1-4d81-967c-164ef0840927
96 http://purl.org/phenoscape/uuid/fce83015-1459-46b9-998e-2237d961f90b
97 http://purl.org/phenoscape/uuid/6902ed68-3e01-4b3b-adbf-ac63aa9a2522
98 http://purl.org/phenoscape/uuid/d3900fea-d545-4e2a-ac51-a8ce112ce36c
99 http://purl.org/phenoscape/uuid/f39d8620-21bf-4b30-9d2b-c8c292253574
100 http://purl.org/phenoscape/uuid/b2d67542-490e-42f9-8bfa-ce80bdef7af5
101 http://purl.org/phenoscape/uuid/dccc11c2-a342-4c13-9677-28179d4522ea
102 http://purl.org/phenoscape/uuid/77e434fe-d94b-449c-b2f5-a4c955f22ee4
103 http://purl.org/phenoscape/uuid/f2d2eb7f-0956-4e8e-8be8-86c9a20cf24a
104 http://purl.org/phenoscape/uuid/d74bfb1d-1fee-4fed-b4c7-4456994dea17
105 http://purl.org/phenoscape/uuid/c4481873-f96f-4b3c-83d6-1e1afd225fe8
106 http://purl.org/phenoscape/uuid/aa65952a-fcb3-4245-aafa-019ea400c018
107 http://purl.org/phenoscape/uuid/632a52dd-a5f7-47f9-a0c7-b7706ebe0873
108 http://purl.org/phenoscape/uuid/1ec151d2-61b5-44f7-a4c3-09e594d2c4fe
109 http://purl.org/phenoscape/uuid/5c7de91c-e120-4477-a50b-95d02c82802d
110 http://purl.org/phenoscape/uuid/011e0f69-4d2a-4870-a876-ebb45a6977fd
111 http://purl.org/phenoscape/uuid/82c33135-8479-4512-b4ac-81a36b93d416
112 http://purl.org/phenoscape/uuid/8e24a21e-58c5-481e-bfd5-3cc6781c7fd0
113 http://purl.org/phenoscape/uuid/6d802c7d-cb3f-4149-95ad-fcfe97a22199
114 http://purl.org/phenoscape/uuid/8f9ae87b-b70d-4e86-a46f-4cb312a2daa2
115 http://purl.org/phenoscape/uuid/924233c8-1023-4c4a-842a-4b2a39b1e3a3
char
1 character_9bd0cd96-aa92-4a07-b735-83be9046467e
2 character_1b7cb4d8-2021-4fe6-a43a-a32d6be9879e
3 character_edea1753-087e-4f7c-8d5d-472fbe2c8f38
4 character_9f3e078d-05fd-465f-b137-227d6fb847d9
5 character_31d06b95-7175-4c5a-8f92-3de324699507
6 character_08f231b3-5277-4e39-8274-e459e22ed50b
7 character_b0c132d0-cb3e-45ef-9923-e5adb5c81c33
8 character_3cf98f1c-ddeb-4f17-9fc7-facb54f796d6
9 character_8b984cd3-8abf-4def-a155-6871ea55e12f
10 character_6a96634e-571c-491b-83b8-fbf00ef66b08
11 character_9632d682-1047-4bde-bbc7-36fdbf85a54d
12 character_4817cbc6-bb97-42ac-8f0e-f8984f248108
13 character_06d80696-5895-4319-aaea-af16031ab4d0
14 character_35a576be-d910-4ac2-9fbb-5edca040e666
15 character_3f936539-a466-40a3-b9de-ed2823acfef0
16 character_2e74855c-c9ab-456c-96ba-3174bbf38640
17 character_67abdd5b-26fc-4268-8081-0faaa7de95d3
18 character_af482a4b-8bf3-460c-8480-ed5f4371eabf
19 character_c1b94d1e-0034-46c1-8df1-1f1873965fd2
20 character_72acbafe-a795-4a1d-ab84-334823b3d64a
21 character_5bfd1b60-95ec-4aae-8bae-a40cd9b9dd68
22 character_06112e2b-ad31-46d5-ba62-2915b406f11f
23 character_4b23b49f-b5e9-403c-88b0-fff8682defff
24 character_8921f55d-f862-497d-9928-78afdba5bc76
25 character_a64d90c6-8812-4d76-8e5e-e53af634d90e
26 character_5de9ebe7-31b0-4b42-b3ff-75e740a0ad69
27 character_44364d1d-feec-43ba-8bb8-a582bb8a0c95
28 character_1471e393-2c3c-4f4f-bd9e-2a181a334bb0
29 character_f84e9329-22c6-4153-a7cd-b6dadac78797
30 character_cefb1207-d06d-4c51-8d31-746f8c45366d
31 character_86d0ad2a-18e6-4492-881f-0dfb78cc79ed
32 character_6a21e09c-b419-4440-9453-88f4af407634
33 character_b0c1441d-be32-48fb-9caf-d1a16fa620c1
34 character_f3eb6a6f-4e68-487f-81bc-5fb4b54fefa2
35 character_37c90967-2d76-4e6f-a2a1-4b23b8077215
36 character_59b8c211-5362-4688-93ed-a1934a0bc210
37 character_6adbccb6-4334-41f7-9b5c-4d7339583615
38 character_a13918b0-22ae-40f5-8944-e486ba5f758a
39 character_db89288d-48ca-4a85-aa81-d1f879c98bca
40 character_6b785c32-5594-4d44-8aab-e6ece6127576
41 character_73ea684b-3ff4-46b9-8d26-4715edb95fe6
42 character_bf19c26b-f90d-486a-965a-423643b3c19d
43 character_85df5d1f-c4b3-4fae-a9df-caa543ebd4ba
44 character_fa194b1e-c8ff-4c33-975b-26088f94913f
45 character_fc790818-0b93-4c03-90cf-2a559f9a2a0c
46 character_7ddf09bb-9cde-4f28-8cb5-a1c193902043
47 character_557d620c-2258-4c83-b0c4-18c86ddb8996
48 character_1e8a28f0-8cdf-48a1-996e-72c08ecd6a76
49 character_d9a40e4c-dc80-4ff0-83e6-e87f164f6380
50 character_fd886612-8267-4264-8376-f64198c2baf4
51 character_e18c6a01-9d21-4414-bd25-2b6d018d9a44
52 character_fd2d9e87-6d88-426c-9303-e45e4a44cb7f
53 character_2b18f56e-b905-467b-a87d-9fae1afd8cb6
54 character_0a57d181-8fce-4369-a269-8a99f0c0497d
55 character_1bc46b91-d002-4b02-a7a8-5015e5c0c8b1
56 character_cd813fd5-7c0e-4809-b792-bac70553f7aa
57 character_3eb6cabd-53b2-4718-8f0b-c979ca254a9c
58 character_85d49b45-8533-414c-ba4a-1d3b891e7dd5
59 character_1a287cc8-4ac0-4186-9e0f-dc559774aa4c
60 character_4a79b12e-a2df-4f05-8746-31f8099fb5a7
61 character_8af59038-a60f-44cd-9622-f5c4859d2a66
62 character_ef4f6ae5-9e9c-4573-9c34-2356df3ae1f3
63 character_4d55179f-2e34-4b48-89bc-023651b71817
64 character_01c88315-39f8-40d0-978a-99ce023e5275
65 character_2b8d92c5-7577-4f67-a9b6-9b0589eba527
66 character_6816f8a0-a363-4c0b-81be-1637206b50af
67 character_da196539-ab59-4623-9603-00698c2c6a41
68 character_816d02e4-1a66-42b2-aefc-c52a4f205290
69 character_e4ef701b-0478-4228-a3d0-c43d8e7ddfa1
70 character_4466d0a0-51b3-4170-a2e7-06d71fb3cf29
71 character_4aba4f0f-e255-4889-b539-6555add1d224
72 character_bc80fa8b-7698-4826-949c-c99a1bd9570f
73 character_8047cf82-64b8-46d5-8916-73a69aafb89c
74 character_32c0de56-6241-4e37-94cc-f9db71589792
75 character_029da492-9a53-4d1a-ac08-9911d1a96547
76 character_ddb9635b-c8a9-4c48-81fb-74ef99451625
77 character_553b042f-3842-46b5-b82f-2bc3fb0bf5d5
78 character_01c7ff7e-05c5-46c3-ba69-da13bf47706e
79 character_5a7b69c8-6a9e-4862-9446-7b75c7976c86
80 character_b96631f3-1aee-4311-b9f0-98091d986e59
81 character_a7353b65-c3ad-46bc-be2c-588975f81dc2
82 character_5bcbfe0a-c228-423c-8c12-0cb98bb25278
83 character_c5edbee4-d875-4a6f-aa7f-fc510a448f0a
84 character_ed9eb74a-d65e-46ec-bb4b-3e423fd8e06c
85 character_dbb23ba8-6769-4700-9a36-aa586470a6d3
86 character_fdd1cba3-aa32-4383-8356-1282d22ed6fb
87 character_53ab4334-76e7-41d9-9398-6814e8f4116c
88 character_e55e3b61-2e71-4e87-a042-e8d658541b9a
89 character_ec28bc1f-f0f4-4784-ae05-bb0c97220f50
90 character_1c9ed314-0818-4cb9-96d6-1ea7d518ddb4
91 character_d32c94f0-d162-47b2-bb8c-4a67f2ccae05
92 character_183dd8fc-df38-4b38-80d8-174671e58d5e
93 character_cad610c6-0793-40eb-9cef-3a94f9e42393
94 character_e006d5d6-bd1e-4124-8d7e-fae870ce39d2
95 character_bad0e4a4-deee-475d-9bae-008320819dca
96 character_1a4924ce-7f0f-46ef-8428-4dc2cdb11b33
97 character_e4906d09-cf40-4861-9a5a-a905857a4937
98 character_e574d5fa-57f4-451a-ad44-28685631c214
99 character_1da4b0d1-4191-481f-92cb-b574f0dd8ea1
100 character_c05c4fcf-80ea-4142-8d45-e59fb424c0e2
101 character_ed98aabf-31fd-498d-b245-51bba8538904
102 character_74d73298-187c-4b1f-b8f8-2aa67935dbae
103 character_683b6dc4-87c5-4293-8a8f-01d18f4958b6
104 character_c5b5d69e-cd02-4301-9a59-8e4bbf27e2e2
105 character_71b71e02-e316-44b4-84f2-ba15c93a2a9f
106 character_9e425775-0ff5-46a1-b30f-7cff0298fd7e
107 character_eb2f5afb-8067-401c-aed8-6dfc4ab850cd
108 character_a68421df-7da8-4bbe-8170-5be8db4989a6
109 character_193f94df-1659-48e8-9eff-af3f8683d8b5
110 character_5e770d08-4a93-47a0-8e23-3289f372b5be
111 character_d8ab1c12-d853-4043-b115-38be317078e7
112 character_46b7b884-5ada-4014-a06a-f1706a72cba0
113 character_f6fa2f2b-10d3-4016-aa17-20a4c4b0de4c
114 character_b2fb860b-6b2f-4185-8955-24d8d3e3c8d8
115 character_d1b62841-b3f4-4f4f-b84b-d7cbd3db5bedA matrix obtained from Phenoscape can be subsetted (filtered) by
taxonomic subgroup or anatomical part. For example, using
is_descendant and is_ancestor methods, a
matrix can be subsetted to a taxonomic subgroup that is the
descendants/ancestors of a given taxon.
m # original character matrix taxa otu otus
1 Ameiurus brunneus VTO_0036273 tcb028860-571e-478a-9449-947a521946a1
2 Ameiurus catus VTO_0036275 tcb028860-571e-478a-9449-947a521946a1
3 Ameiurus melas VTO_0036272 tcb028860-571e-478a-9449-947a521946a1
4 Ameiurus natalis VTO_0036274 tcb028860-571e-478a-9449-947a521946a1
5 Ameiurus nebulosus VTO_0036278 tcb028860-571e-478a-9449-947a521946a1
6 Ameiurus platycephalus VTO_0036276 tcb028860-571e-478a-9449-947a521946a1
7 Ameiurus serracanthus VTO_0036277 tcb028860-571e-478a-9449-947a521946a1
8 Ictalurus australis VTO_0061495 tcb028860-571e-478a-9449-947a521946a1
9 Ictalurus balsanus VTO_0036221 tcb028860-571e-478a-9449-947a521946a1
10 Ictalurus dugesii VTO_0061497 tcb028860-571e-478a-9449-947a521946a1
11 Ictalurus furcatus VTO_0036223 tcb028860-571e-478a-9449-947a521946a1
12 Ictalurus lupus VTO_0036220 tcb028860-571e-478a-9449-947a521946a1
13 Ictalurus mexicanus VTO_0061498 tcb028860-571e-478a-9449-947a521946a1
14 Ictalurus pricei VTO_0036218 tcb028860-571e-478a-9449-947a521946a1
15 Ictalurus punctatus VTO_0036225 tcb028860-571e-478a-9449-947a521946a1
anterior dentation of pectoral fin spine
1 1
2 1
3 NA
4 NA
5 1
6 1
7 1
8 1
9 0
10 NA
11 0
12 1
13 NA
14 1
15 1
anterior distal serration of pectoral fin spine
1 1
2 1
3 0 and 1
4 1
5 1
6 1
7 1
8 1
9 0 and 1
10 1
11 1
12 1
13 1
14 1
15 1
(is_desc <- is_descendant('Ictalurus', m$taxa)) [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE
[13] TRUE TRUE TRUE
m[is_desc, ] #subsetting to the descendants of Ictalurus taxa otu otus
8 Ictalurus australis VTO_0061495 tcb028860-571e-478a-9449-947a521946a1
9 Ictalurus balsanus VTO_0036221 tcb028860-571e-478a-9449-947a521946a1
10 Ictalurus dugesii VTO_0061497 tcb028860-571e-478a-9449-947a521946a1
11 Ictalurus furcatus VTO_0036223 tcb028860-571e-478a-9449-947a521946a1
12 Ictalurus lupus VTO_0036220 tcb028860-571e-478a-9449-947a521946a1
13 Ictalurus mexicanus VTO_0061498 tcb028860-571e-478a-9449-947a521946a1
14 Ictalurus pricei VTO_0036218 tcb028860-571e-478a-9449-947a521946a1
15 Ictalurus punctatus VTO_0036225 tcb028860-571e-478a-9449-947a521946a1
anterior dentation of pectoral fin spine
8 1
9 0
10 NA
11 0
12 1
13 NA
14 1
15 1
anterior distal serration of pectoral fin spine
8 1
9 0 and 1
10 1
11 1
12 1
13 1
14 1
15 1Search for details for a given taxon:
taxon_info("Coralliozetus") id label extinct
1 http://purl.obolibrary.org/obo/VTO_0042955 Coralliozetus FALSE
rank.id rank.label common_name
1 http://purl.obolibrary.org/obo/TAXRANK_0000005 genus <NA>Search for details for a given anatomical structure:
anatomy_term_info("basihyal bone") label isDefinedBy
1 basihyal bone http://purl.obolibrary.org/obo/uberon.owl
definition
1 Replacement bone that is median and is the anterior-most bone of the ventral hyoid arch.
id
1 http://purl.obolibrary.org/obo/UBERON_0011618Resolve a given term to its IRI:
get_term_iri("Coralliozetus", "vto")[1] "http://purl.obolibrary.org/obo/VTO_0042955"
get_term_iri("basihyal bone", "uberon")[1] "http://purl.obolibrary.org/obo/UBERON_0011618"Test if a taxon is extinct:
is_extinct("Fisherichthys")Fisherichthys
TRUE