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.

Installation

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:

Character Matrix via OntoTrace

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] 2

More 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                                               1

The 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_2002002

Character Matrices for Studies

To 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 serrae

Each 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-d7cbd3db5bed

Obtain Other Data

Subsetting a Matrix

A 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                                               1

Search 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_0011618

Miscellaneous methods:

Resolve 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