Package 'OmaDB'

Title: R wrapper for the OMA REST API
Description: A package for the orthology prediction data download from OMA database.
Authors: Klara Kaleb
Maintainer: Klara Kaleb <[email protected]>, Adrian Altenhoff <[email protected]>
License: GPL-3
Version: 2.23.0
Built: 2024-10-30 08:28:16 UTC
Source: https://github.com/bioc/OmaDB

Help Index

OmaDB: A package for the orthology prediction data download from OMA database.

Description

OmaDB is a wrapper for the REST API for the Orthologous MAtrix project (OMA) which is a database for the inference of orthologs among complete genomes. For more details on the OMA project, see https://omabrowser.org/.

OmaDB functions

The package contains a range of functions that are used to query the database. Some of the main functions are listed below:

  • getProtein()

  • getHOG()

  • getOMAGroup()

  • getGenomePairs()

  • getTaxonomy()

  • mapSequence()

  • annotateSequence()

  • searchProtein()

In addition to these, OmaDB features a range of functions that are used to format the retrieved data into some commonly used Bioconductor objects using packages such as GenomicRanges, Biostrings, topGO and ggtree. Some of them are listed below:

  • formatTopGO()

  • getGRanges()

The above functions are described in more detail in the package vignette's listed below:

  • Get started with OmaDB

  • Exploring Hierarchical orthologous groups with OmaDB

  • Exploring Taxonomic trees with OmaDB

  • Sequence Analysis with OmaDB

Resolve URLs automatically when accessed

Description

The function to obtain further information from a given url.

Usage

## S3 method for class 'omadb_obj'
x$name

Arguments

x

object
name

attribute

Value

API response behind the URL

Map GO annotation to a sequence that is not available in the OMA Browser

Description

This function obtain Gene Ontology annotation for a given sequence that does not need to exist in the OMA Browser so far. The query sequence will analysed and a fast homology detection approach based on kmers will be used to detect the closest sequences in OMA. GO annotations for these top hits will be used to annotated the query sequence.

Usage

annotateSequence(query)

Arguments

query

the sequence to be annotated, it can be either a string or an AAString object from the Biostrings package

Value

a data.frame containing the the GO annotation information of the most similar protein to the query sequence

Examples

annotateSequence(query='MNDPSLLGYPNVGPQQQQQQQQQQHAGLLGKGTPNALQQQLHMNQLTGIPPPGLMNNSDVHTSSNNNSRQLLDQLANGNANMLNMNMDNNNNNNNNNNNNNNNGGGSGVMMNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQSLGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHERRFIEINTDGEPQREYDSLQQSTEHLATDLAKRTFTVLSYNTLCQHYATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQEGNGRDFGYMSEKNFSHNLALKSSYNCIGELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFEFMKTNTGSKKV')

Format the GO annotations data

Description

The function to create a list of GO annotations that is compatible with topGO from protein objects in roma

Usage

formatTopGO(geneList, format)

Arguments

geneList

the list of OmaDB protein objects or a dataframe of ontologies to be included in the analysis - this is where the GO annotations are extracted from.
format

format for the data to be returned in - either 'GO2geneID' or 'geneID2GO'

Value

a list containing the GO2geneID or geneID2GO information

Examples

geneList = list(getProtein(id='YEAST01'),getProtein(id='YEAST03'))
annotations = formatTopGO(geneList,format='geneID2GO')

Get the value for the Object Attribute

Description

The function to obtain the value for an object attribute.

Usage

getAttribute(obj, attribute)

Arguments

obj

the object of interest
attribute

the attribute of interest

Value

an value for a given object attribute

Examples

members = getAttribute(getOMAGroup(id ='YEAST58'),'members')

Retrieve a genome from the OMA Browser database

Description

This function obtains the basic information for one specific genome available on the OMA Browser, or - if no id is provided - a dataframe with all available genomes.

Usage

getGenome(id = NULL, attribute = NULL)

Arguments

id

A genome identifier. By default, all available genomes will be returned.
attribute

An extra attribute to be returned (proteins)

Details

Ids can be either the scientific name of a species, the NCBI taxonomy id or the UniProtKB mnemonic species code.

The optional argument attribute can be used to directly load the proteins belonging to the genome. Alternatively, you can access the proteins attribute of the result which will transparently load the proteins from the OMA Browser.

Value

an object containing the JSON keys as attributes or a dataframe

Examples

getGenome()
getGenome(id='HUMAN')
getGenome(id=9606)
getGenome(id='HUMAN',attribute='proteins')

Retrieves the pairwise relations among two genomes

Description

This function retrieves the pairwise relations among two genomes from the OMA Browser database. The relations are orthologs in case the genomes are different and "close paralogs" and "homoeologs" in case they are the same.

Usage

getGenomePairs(genome_id1, genome_id2, chr1 = NULL, chr2 = NULL,
  rel_type = NULL, ...)

Arguments

genome_id1

an identifier for the first genome, which can be either its taxon id or UniProt species code
genome_id2

an an identifier for the second genome, which can be either its taxon id or UniProt species code
chr1

the chromosome of interest for the first genome
chr2

the chromosome of interest for the second genome
rel_type

the pairs relationship type
...

qwargs

Details

By using the parameters chr1 and chr2, one can limit the relations to a certain chromosome for one or both genomes. The id of the chromosome corresponds to the chromosome ids from the getGenome result.

The rel_type parameter further limits the returned relations to a specific subtype of orthologs (i.e. "1:1", "1:n", "m:1", "m:n") or - within a genome to either "close paralogs" or "homeologs".

Value

a dataframe containing information about both the entries in the orthologous pair and their relationship

Examples

getGenomePairs(genome_id1='YEAST',genome_id2='ASHGO')

Retrieve a HOG from the OMA Browser

Description

The function retrieves a specific Hierarchical Orthologous Group (HOG) from the OMA Browser database. A HOG is a set of genes that have all decendet from a single ancestral gene at a specific taxonomic level.

Usage

getHOG(id, level = NULL, members = FALSE)

Arguments

id

an identifier for the HOG to be returned - either its HOG ID or a protein id.
level

a specific level for the HOG to be restricted to. level can either be 'root', or the name of a taxonomic level that is part of the HOG, e.g. 'Fungi'. By default it will retrieve the depest level of the most specific subhog for the given ID.
members

boolean that when set to TRUE returns a dataframe containg the protein members at a given hog level

Details

A HOG can be identified by its member proteins and a taxonomic level, or a HOG ID. As a taxonomic level, you can use either 'root' to retrieve the HOG at its deepest level, or the name of NCBI taxonomy level, or leave it out in which case the deepest level that doesn't include a duplication node is used.

The function either returns a single hog object or a list of hog objects. The later happens if the HOG ID you provide has already split into several sub-hogs at the level you indicate.

Value

an object containing HOG attributes, or a list of those

Examples

getHOG(id = 'YEAST590')
getHOG(id = 'YEAST590', level='root')
getHOG(id = 'YEAST590', level='Saccharomycetaceae', members=TRUE)

Get loci for a given list of proteins

Description

Function to obtain loci in genomic range format for a given list of proteins

Usage

getLocus(proteins)

Arguments

proteins

the dataframe or a list of dataframes containing the protein data of interest. this can either be the members df or a list of protein ids.

Value

genomic range object from the GenomicRanges package in Bioconductor

Examples

loci = getLocus(proteins = getOMAGroup('YEAST58')['members'])

Get the Object Attributes

Description

The function to obtain the attributes and their data types for the object created.

Usage

getObjectAttributes(obj)

Arguments

obj

the object of interest

Value

an list of object attributes and their data classes

Examples

attributes = getObjectAttributes(getOMAGroup(id ='YEAST58'))

Retrieve an OMA Group from the OMA Browser

Description

This function obtains an OMA Group from the OMA Browser database. An OMA Group is defined to be a clique of proteins that are all orthologous to each other, i.e. they are all related through speciation events only. An OMA Group can thus by definition not contain any inparalogs. It is a very stringent orthology grouping approach. OMA Groups are mostly useful to infer phylogenetic species tree where they can be used as marker genes.

Usage

getOMAGroup(id, attribute = NULL)

Arguments

id

An identifier for the group. See above for possible types of IDs.
attribute

an extra attribute to be returned (close_groups)

Details

Retrieving an OMA Group can be done using a group nr as id, its fingerprint (a 7mer AA sequence which is unique to proteins in that group), a member protein id or any sequence pattern that is unique to the group.

Value

an object containing the JSON keys as attributes or a dataframe

Examples

getOMAGroup(id='58')
getOMAGroup(id='P12345')
getOMAGroup(id='NNRRGRI')
getOMAGroup(id='58', attribute='close_groups')

Retrieve a protein from the OMA Browser

Description

This function enables to retrieve information on one or several proteins from the OMA Browser database.

Usage

getProtein(id, attribute = NULL)

Arguments

id

Identifier(s) for the entry or entries to be returned. a character string if single entry or a vector if multiple.
attribute

Instead of the protein, return the attribute property of the protein. Attriute needs to be one of 'domains', 'orthologs', 'gene_ontology', 'locus', or 'homoeologs'.

Details

In its simplest form the function returns the base data of the query protein. The query protein can be selected with any unique id, for example with a UniProtKB accession (P12345), an OMA id (YEAST00012), or a RefSeq id (NP_001226). To retrieve more than one protein, you should pass a vector of IDs.

Non-scalar properties of proteins such as their domains, GO annotations, orthologs or homeologs will get loaded upon accessing them, or if you only need this information you can set the attribute parameter to the property name and retrieve this information directly.

Value

An object containing the JSON keys as attributes or a dataframe containing the non-scalar protein property.

See Also

For non-unique non-unique IDs or partial ID lookup, use searchProtein instead.

Examples

getProtein(id='YEAST00001')
getProtein(id='YEAST00001', attribute='orthologs')
getProtein(id=c('YEAST00001','YEAST00002','YEAST00012'))
getProtein(id=c('YEAST00001','YEAST00002','YEAST00012'), attribute='gene_ontology')

Get the Taxonomic tree function

Description

The function to obtain the taxonomic tree from the database in the newick format that can be plugged into phylo.io for visualisation.

Usage

getTaxonomy(root = NULL, members = NULL, newick = TRUE)

Arguments

root

optional parameter, the root of the node of interest
members

optional parameter, list of member ncbi taxon or UniProt IDs that should be included in the induced taxonomy.
newick

optional parameter, boolean default set to TRUE

Value

an object containing the JSON keys as attributes

Examples

getTaxonomy()
getTaxonomy(members='YEAST,ASHGO')
getTaxonomy(root='Alveolata')

Get the topGO Object function

Description

The function to create a topGO object containing the GO annotations for the given protein list.

Usage

getTopGO(annotations, format, foregroundGenes, ontology)

Arguments

annotations

list of GO annoatations obtained from the formatTopGO()
format

Format for the data to be returned in - either 'GO2geneID' or 'geneID2GO'
foregroundGenes

List of identifiers for the foreground genes
ontology

The ontology for which the enrichment should be done. This parameter is passed directly to the topGOdata constructor.

Value

topGO object

Examples

geneList = list(getProtein(id='YEAST58'),getProtein(id='YEAST00059'))
annotations = formatTopGO(geneList,format='geneID2GO')
library(topGO)
getTopGO(annotations, foregroundGenes = list('YEAST00058'), format = 'geneID2GO', ontology = 'BP')

Get the Tree Object

Description

A convenience function to obtain a tree object from newick tree, essentially wraps read.tree from the ape package.

Usage

getTree(newick)

Arguments

newick

The newick tree to be instantiated.

Value

a tree object

Examples

taxonomy = getTaxonomy(root='Alveolata')
getTree(newick=taxonomy$newick)

Get the API and database version function

Description

The function to obtain the API and database version that the package is using.

Usage

getVersion()

Value

S3 object

Examples

getVersion()

An example OMA group object.

Description

An object containing information for the OMA group number 737636.

Usage

group

Format

An S3 object with 4 variables:

group_nr

group number, not stable across releases

fingerprint

fingerprint of the oma group, stable across releases

related_groups

url to the endpoint containing the list of oma groups that share some of the orthologs with this oma group

members

list of protein members of this oma group

...

Source

https://omabrowser.org/api/group/YEAST58/

An example HOG object.

Description

An object containing information for the HOG:0273533.1b.

Usage

hog

Format

An S3 object with 8 variables:

hog_id

hog identifier

level

the taxonomic level of this hog

levels_url

url pointer to the hog information at a given level

members_url

url pointer to the list of gene members for this hog

alternative_members

a dataframe object containing the rest of the taxonomic levels in this hog

roothog_id

the root taxonomic level of this hog

parent_hogs

a dataframe containing information on the parent hogs to the current hogs

children_hogs

a dataframe containing information on the children hogs to the current hogs

...

Source

https://omabrowser.org/api/hog/HOG:0273533.1b/

Map the Protein Sequence Function

Description

The function to identify a sequence.

Usage

mapSequence(query, search = NULL, full_length = FALSE)

Arguments

query

the sequence to be searched, it can be either a string or an AAString object from the Biostrings package
search

argument to choose search strategy. Can be set to 'exact', 'approximate' or 'mixed'. Defaults to 'mixed', meaning first tries to find exact match. If no target can be found, uses approximate search strategy to identify query sequence in database.
full_length

a boolean indicating whether or not for exact matches, the query sequence must be matching the full target sequence. By default, a partial exact match is also reported as exact match.

Value

a data.frame containing the information of matches for the query sequence

Examples

mapSequence(query='MNDPSLLGYPNVGPQQQQQQQQQQHAGLLGKGTPNALQQQLHMNQLTGIPPPGLMNNSDVHTSSNNNSRQLLDQLANGNANMLNMNMDNNNNNNNNNNNNNNNGGGSGVMMNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQSLGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHERRFIEINTDGEPQREYDSLQQSTEHLATDLAKRTFTVLSYNTLCQHYATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQEGNGRDFGYMSEKNFSHNLALKSSYNCIGELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFEFMKTNTGSKKV')
mapSequence(search='mixed',query='NKLLQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHERRFIEINTDGEPQREYDSLQQSTEHLATDLAKRTFTVLSYNTLCQHYATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQEGNGRDFGYMSEKNFSHNLALKSSYNCIGELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFEFMKTNTGSKKV')

An example orthologs object.

Description

A dataframe containing information for the orthologs of protein YEAST00058.

Usage

orthologs

Format

A dataframe object with 15 variables:

entry_nr

entry number of the ortholog

omaid

oma identifier of the ortholog

canonicalid

canonicalid of the ortholog

sequence_md5

sequence_md5 of the ortholog

oma_group

oma_group of the ortholog

oma_hog_id

hog id of the ortholog

chromosome

chromosomal location of the ortholog

locus.start

start locus of the ortholog

locus.end

end locus of the ortholog

locus.strand

locus strand of the ortholog

is_main_isoform

true/false

rel_type

relationship type of the ortholog to the gene

distance

ortholog distance

score

ortholog score

...

Source

https://omabrowser.org/api/protein/YEAST00058/orthologs

An example genome alignment object.

Description

A dataframe containing information for the whole genome aligment of YEAST and ASHGO.

Usage

pairs

Format

A dataframe object with 12 variables for each member of the pair, as well some 3 additional variables:

entry_nr

entry number of the ortholog

omaid

oma identifier of the ortholog

canonicalid

canonicalid of the ortholog

sequence_md5

sequence_md5 of the ortholog

oma_group

oma_group of the ortholog

oma_hog_id

hog id of the ortholog

chromosome

chromosomal location of the ortholog

locus.start

start locus of the ortholog

locus.end

end locus of the ortholog

locus.strand

locus strand of the ortholog

is_main_isoform

true/false

rel_type

relationship type of the ortholog to the gene

distance

ortholog distance

score

ortholog score

...

Source

https://omabrowser.org/api/pairs/YEAST/ASHGO/

An example protein object.

Description

An object containing information for the YEAST00058 protein.

Usage

protein

Format

A S3 object with 23 variables:

entry_nr

entry number of the protein

entry_url

url pointer to the protein

omaid

oma identifier of the protein

canonicalid

canonicalid of the protein

sequence_md5

sequence_md5 of the protein

oma_group

oma_group of the protein

oma_hog_id

hog id of the protein

chromosome

chromosomal location of the protein

locus

GRanges object with the locus information for the protein

is_main_isoform

true/false

roothog_id

root taxonomic level of the relevant hog

roothog_id

taxonomic levels of the hog in which the protein is present

sequence_length

length of the protein sequence

sequence

AAString of the protein sequence

cdna

DNAString of the protein sequence

domains

url pointer to the list of protein domains

xref

url pointer to the list of protein cross references

orthologs

url pointer to the list of protein orthologs

homeologs

url pointer to the list of protein homeologs

gene_ontology

url pointer to the list of protein GO ontologies

oma_group_url

url pointer to the protein oma group

oma_hog_members

url pointer to the protein hog members

alternative_isoforms_urls

list of url pointers to the protein isoforms

...

Source

https://omabrowser.org/api/protein/6633022/

Load data for a given url from the OMA Browser API.

Description

This function is usualy not needed by users. In most circumstances an attribute containing a URL is automatically loaded when accessed. However, in case the data is transformed into a dataframe, this will no longer be true, in which case one can access the data behind this attribute using this function.

Usage

resolveURL(url)

Arguments

url

The url of interest

Value

a data.frame containing the information behind an URL

Examples

resolveURL('http://omabrowser.org/api/protein/YEAST58/gene_ontology/')

Get the CrossReferences in the OMA database for a pattern

Description

The function to list all the crossreferences that match a certain defined pattern.

Usage

searchProtein(pattern)

Arguments

pattern

the pattern to query the OMA database with - needs to be at least 3 characters long

Value

a data.frame containing information on the cross references for a given pattern

Examples

searchProtein(pattern='MAL')

An example dataframe containing GO annotations identified from a given sequence.

Description

An example dataframe containing GO annotations identified from a given sequence.

Usage

sequence_annotation

Format

A dataframe with 13 variables:

Qualifier

qualifier of the annotation

GO_ID

GO term for the annotation

With

GO term for the annotation

Evidence

evidence for the annotation

Date

date

DB_Object_Type

identified object type

DB_Object_Name

identified object name

Aspect

aspect

Assigned_By

assignment of the annotation

GO_name

GO term name

DB

database

DB.Reference

database reference

Synonym

synonym

...

Source

https://omabrowser.org/api/function/?query=MNDPSLLGYPNVGPQQQQQQQQQQHAGLLGKGTPNALQQQLHMNQLTGIPPPGLMNNSDVHTSSNNNSRQLLDQLANGNANMLNMNMDNNNNNNNNNNNNNNNGGGSGVMMNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQSLGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHER

An example dataframe containing proteins identified from a given sequence.

Description

An example dataframe containing proteins identified from a given sequence.

Usage

sequence_map

Format

A dataframe with 3 variables:

query

sequence that was queried

identified_by

type of identification

targets

list of protein targets identified

...

Source

https://omabrowser.org/api/sequences/?query=MNDPSLLGYPNVGPQQQQQQQQQQHAGLLGKGTPNALQQQLHMNQLTGIPPPGLMNNSDVHTSSNNNSRQLLDQLANGNANMLNMNMDNNNNNNNNNNNNNNNGGGSGVMMNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQSLGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHER

Set the url to the OMA Browser API

Description

Function to set the base url to the OMA Browser API. If no url is specified, the default OMA Browser API url is used.

Usage

setAPI(url)

Arguments

url

Base url to the API

An example newick format taxonomy object.

Description

An example newick format taxonomy object.

Usage

taxonomy

Format

An S3 with 2 variables:

root_taxon

sequence that was queried

newick

taxonomy newick

...

Source

https://omabrowser.org/api/taxonomy/Alveolata/?type=newick

An example xref object.

Description

An example xref object.

Usage

xref

Format

A dataframe with 8 variables:

xref

cross reference

source

source of the cross reference

entry_nr

oma database entry number

oma_id

oma id of the cross reference

genome.code

genome_id of the cross reference

genome.taxon_id

taxon_id of the cross reference

genome.species

species of the cross reference

genome.genome_url

genome url pointer of the cross reference

...

Source

https://omabrowser.org/api/xref/?search=MAL