ontotext Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Get ontology term(s) original full text Description ontotext reads one or more complete ontology term entries from a database or a file and writes them to a text file. Optionally, the first ontology term from the input stream only can be retrieved. The complete entry, including heading annotation, is retrieved and written and the data is not altered or reformatted in any way. Usage Here is a sample session with ontotext % ontotext edam:1234 Get ontology term(s) original full text Full text output file [1234.ontotext]: Go to the input files for this example Go to the output files for this example Example 2 % ontotext edam:0850 -subclasses Get ontology term(s) original full text Full text output file [0850.ontotext]: Go to the input files for this example Go to the output files for this example Command line arguments Get ontology term(s) original full text Version: EMBOSS:6.5.6.0 Standard (Mandatory) qualifiers: [-oboterms] obo Obo term filename and optional format, or reference (input query) [-outfile] outfile [*.ontotext] Full text output file Additional (Optional) qualifiers: -subclasses boolean [N] Extend the query matches to include all terms which are specialisations (sub-classes) of the matched terms. -obsolete boolean [N] The default behaviour is to not use or return obsolete terms. This option if set will include all terms. Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-oboterms" associated qualifiers -iformat1 string Input obo format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -idbname1 string User-provided database name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format The input is a standard EMBOSS ontology query. The major ontology sources defined as standard in EMBOSS installations are EDAM, GO (gene Ontology) and SO (Sequence Ontology). Data can also be read from ontology output in "obo" format written by an EMBOSS application. Input files for usage example Database entry: edam:1234 [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data def: Any collection of multiple nucleotide sequences and associated metadata tha t do not (typically) correspond to common sequence database records or database entries. subset: data is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence Input files for usage example 2 Database entry: edam:0850 [Term] id: EDAM_data:0850 name: Sequence set namespace: data def: A collection of multiple molecular sequences and associated metadata that d o not (typically) correspond to molecular sequence database records or entries a nd which (typically) are derived from some analytical method. comment: This concept may be used for arbitrary sequence sets and associated dat a arising from processing. subset: data synonym: "sequence_collection" EXACT [SO:0001260] is_a: EDAM_data:2955 ! Sequence report Output file format ontotext reports the full text of the input ontology terms. Output files for usage example File: 1234.ontotext [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data subset: data def: "Any collection of multiple nucleotide sequences and associated metadata th at do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence Output files for usage example 2 File: 0850.ontotext [Term] id: EDAM_data:0850 name: Sequence set namespace: data subset: data def: "A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method." [http://edamonto logy.org] comment: This concept may be used for arbitrary sequence sets and associated dat a arising from processing. synonym: "sequence_collection" EXACT [SO:0001260] is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data subset: data def: "Any collection of multiple nucleotide sequences and associated metadata th at do not (typically) correspond to common sequence database records or database entries." [http://edamontology.org] is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:1239 name: Restriction digest namespace: data subset: data def: "Restriction digest fragments from digesting a nucleotide sequence with res triction sites using a restriction endonuclease." [http://edamontology.org] xref: SO:0000412 is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:1240 name: PCR primers namespace: data subset: data def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a min imal primer set." [http://edamontology.org] is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:1246 name: Sequence cluster (nucleic acid) namespace: data subset: data def: "A cluster of nucleotide sequences." [http://edamontology.org] comment: The sequences are typically related, for example a family of sequences. synonym: "Nucleotide sequence cluster" EXACT [http://edamontology.org] is_a: EDAM_data:1234 ! Sequence set (nucleic acid) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:0925 name: Sequence assembly [Part of this file has been deleted for brevity] def: "A set of sequences that have been clustered or otherwise classified as bel onging to a group including (typically) sequence cluster information." [http://e damontology.org] comment: The cluster might include sequences identifiers, short descriptions, al ignment and summary information. is_a: EDAM_data:0850 ! Sequence set relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification relationship: has_topic EDAM_topic:0724 ! Protein families [Term] id: EDAM_data:1245 name: Sequence cluster (protein) namespace: data subset: data def: "A cluster of protein sequences." [http://edamontology.org] comment: The sequences are typically related, for example a family of sequences. synonym: "Protein sequence cluster" EXACT [http://edamontology.org] is_a: EDAM_data:1233 ! Sequence set (protein) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data subset: data def: "A collection of sequences output from a bootstrapping (resampling) procedu re." [http://edamontology.org] comment: Bootstrapping is often performed in phylogenetic analysis. is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1233 name: Sequence set (protein) namespace: data subset: data def: "Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database en tries." [http://edamontology.org] is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1238 name: Proteolytic digest namespace: data subset: data def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemica l cleavage) with fragment masses." [http://edamontology.org] is_a: EDAM_data:1233 ! Sequence set (protein) relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:1262 name: Peptide molecular weight hits namespace: data subset: data def: "A report on peptide fragments of certain molecular weight(s) in one or mor e protein sequences." [http://edamontology.org] is_a: EDAM_data:1233 ! Sequence set (protein) Data files The EDAM Ontology is included in EMBOSS as local database edam. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description drtext Get data resource entries complete text edamdef Find EDAM ontology terms by definition edamhasinput Find EDAM ontology terms by has_input relation edamhasoutput Find EDAM ontology terms by has_output relation edamisformat Find EDAM ontology terms by is_format_of relation edamisid Find EDAM ontology terms by is_identifier_of relation edamname Find EDAM ontology terms by name entret Retrieve sequence entries from flatfile databases and files godef Find GO ontology terms by definition goname Find GO ontology terms by name ontocount Count ontology term(s) ontoget Get ontology term(s) ontogetcommon Get common ancestor for terms ontogetdown Get ontology term(s) by parent id ontogetobsolete Get ontology ontology terms ontogetroot Get ontology root terms by child identifier ontogetsibs Get ontology term(s) by id with common parent ontogetup Get ontology term(s) by id of child ontoisobsolete Report whether an ontology term id is obsolete textget Get text data entries textsearch Search the textual description of sequence(s) Author(s) Peter Rice European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None