PhylomeDB web API

URL query term

Value

q

An action to be perform in PhylomeDB (i.e. q=search_tree). Required

  • search_tree for retrieving phylogenetic trees associated to the sequence identifier.
  • seqinfo for retrieving information about the sequence identifier.

seqid

Any sequence identifier (i.e. Uniprot ID, Ensembl ID). Required

Example:

http://phylomedb.org/?q=search_tree&seqid=TP53

phyid

A phylome id (i.e. 102), a list of comma-sepparated phylome ids, or a collection id (i.e. PhyC1).

By default a tree from the most recent phylome will be selected.

method

The preferred evolutionary model for the target tree. Default: best model.

snode

a comma-separated list of target nodes, defined as follows:

node_feature|search_pattern|fgcolor|bgcolor

where node_feature is one of the text based node attributes available:

  • name: Leaf names as shown in the tips of the tree (i.e. TP53)
  • phylomedb_name: phylomedb id format (i.e. Phy00086SJ)
  • gene_name: original ID used in the source proteome (i.e. ORF_1)
  • swissprot_name: a swissprot id (i.e. P04637)
  • trembl_name: a trembl id (i.e. K7PPA8)
  • ensembl_name: any protein, transcript or gene ensembl id (i.e. ENSP00000269305)
  • genolevures_name: An Ascomycete-based Genolevures database id
  • taxid: a NCBI taxa id (i.e. 9606)
  • species: Uniprot species code (i.e HUMAN)
  • spname: Scientific name (i.e sapiens)
  • relative_age: Any of the tracked NCBI taxa names (i.e. Primates

search_pattern must be a text string or a perl regular expression.

 

fgcolor and bgcolor are optional parameters controlling foreground and background colors

of the matching nodes (color should be one of the SVG color names or a RGB color code)

 

Example: 

http://phylomedb.org/?q=search_tree&seqid=TP53&snodes=species|MOUSE|red,best_name|TP73|blue|grey,spname|melano,relative_age|primates|blue|steelblue

tree_features

A comma separated list of tree features to be shown. Currently the following features are

supported: best_name, name, gene_name, swissprot_name, trembl_name, ensembl_name, genolevures_name,

taxid, spname, lineage, motifs and support.

Example:

http://phylomedb.org/?q=search_tree&seqid=TP53&tree_features=best_name,ensembl_name,spname,lineage