Transcript EMBL-EBI Powerpoint Presentation

EMBOSS as a DAS Client
Peter Rice
[email protected]
Mahmut Uludag [email protected]
3rd March 2011.
EBI is an Outstation of the European Molecular Biology Laboratory.
EMBOSS: A quick introduction
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European Molecular Biology Open Software Suite
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Open source package for sequence analysis
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ANSI C source code
GPL licensed applications, LGPL libraries
200+ applications
100+ third party applications in 15 associated packages
Project started 1996 at Sanger Centre and HGMP
Now based at EBI
Release 6.3.0 15th July 2010
Funded by UK-BBSRC and EMBL-EBI
EMBOSS as a DAS Client
EMBOSS history
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Project started at Sanger Centre and SEQNET August 1996
Alan moved from SEQNET 1997 (Wellcome funding)
Peter moved to Lion Bioscience 2000 (CCP11-BBSRC/MRC)
Peter moved to EBI 2003
HGMP closed 2005: Alan+Jon moved to EBI
BBSRC funding (limited) 2006-2009
BBSRC BBR funding 2009-2011
• Major new developments
• New data types
• New data sources
• Built-in ontologies
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EMBOSS as a DAS Client
EMBOSS command line interface
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EMBOSS applications run from the command line
This is not the only interface
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All applications have a command definition file (.acd)
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There are over 100 interfaces and packaged systems available
• Web interfaces
• Graphical user interfaces (GUIs)
• Web services
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Defines all inputs, outputs, and other options
Read at startup
Contains all command line options with descriptions
Template for any other interface
EMBOSS as a DAS Client
EMBOSS command line example
% antigenic
Input protein sequence(s): uniprot:actb1_fugru
Minimum length of antigenic region [6]:
Output report [actb1_fugru.antigenic]:
% antigenic uniprot:actb1_fugru -auto
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EMBOSS ACD File
application: antigenic [
documentation: "Finds antigenic sites in proteins"
groups: "Protein:Motifs"
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section: input [ information: "Input section” type: "page“ ]
seqall: sequence [
parameter: "Y"
type: “proteinstandard"
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integer: minlen [
standard: "Y"
minimum: "1"
maximum: "50"
default: "6"
information: "Minimum length of antigenic region"
]
endsection: required
section: output [ information: "Output section” type: "page” ]
endsection: input
section: required [ information: "Required section” type: "page” ]
report: outfile [
parameter: "Y"
rformat: "motif"
multiple: "Y"
taglist: "int:pos=Max_score_pos"
]
endsection: output
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EMBOSS ACD File with EDAM Annotation
application: antigenic [
documentation: "Finds antigenic sites in proteins"
groups: "Protein:Motifs"
relations: "EDAM:0000201 topic Immunological analysis"
relations: "EDAM:0000416 operation Epitope mapping“
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section: input [ information: "Input section“ type: "page” ]
seqall: sequence [
parameter: "Y"
type: “proteinstandard"
relations: "EDAM:0001219 data Pure protein sequence"
relations: "EDAM:0000849 data Sequence record"
relations: "EDAM:0002178 data 1 or more“
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endsection: input
section: required [ information: "Required section” type: "page” ]
integer: minlen [
standard: "Y"
minimum: "1"
maximum: "50"
default: "6"
information: "Minimum length of antigenic region"
relations: "EDAM:0001249 data Sequence length“
]
endsection: required
section: output [ information: "Output section” type: "page” ]
report: outfile [
parameter: "Y"
rformat: "motif"
multiple: "Y"
taglist: "int:pos=Max_score_pos"
relations: "EDAM:0001534 data Peptide immunogenicity report“
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endsection: output
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Documentation & books
Three books at typesetting stage.
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Administrators’ Manual
Users’ Manual
Developers’ Manual
Concomitant major revision of EMBOSS website.
Automation of website content addition.
Books to form basis of new website content.
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EMBOSS: Sequences
Uniform Sequence Address (USA): URL-style naming
Derived from the familiar "VMS logical name" syntax used by SRS and GCG.
database : entryname
• embl : ecompa
ID or accession can be used in this way
• uniprot-id : opsd_bovin
SRS syntax for query by ID
• embl-acc : x13776
SRS syntax for query by accession
format :: filename
• fasta :: /users/pmr/paamir.fa
Filename with specific format
• ecoompa.genbank
With no format, can try all formats
format :: filename : entryname
• fasta :: unfinished : AH6.1
Most formats allow multiple sequences
Also @listfile
and asis::gctgactgactgatg
Queries database-field:query
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SRS syntax for id, acc, sv, des, key, org
New data resources
• Aim to read “all” public data resources
• Follow cross-references (explicit and implied)
• UniProt
• EMBL/GenBank/DDBJ
• Other
• Servers
• Multiple data resources through a single server definition
• DAS, Ensembl, BioMart, WsEbeye, DbFetch, SRS
• Cache files of resource definitions for server
• Data resource catalogue (drcat)
• 600+ data resources
• Query terms and URLs
• EDAM annotation of resources, formats, identifiers, terms
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Data resource catalogue (drcat)
ID
ArachnoServer
Acc
DB-0145
Name
ArachnoServer
Desc
Spider toxin database
URL
http://www.arachnoserver.org
Cat
Organism-specific databases
Taxon
6845 | Arachnida
EDAMres 0000621 | Organism-specific
EDAMdat 0002400 | Toxin annotation
EDAMid 0002578 | ArachnoServer ID
Xref
SP_explicit | ArachnoServer ID;Toxin name
Query
Toxin annotation | HTML | ArachnoServer ID |
www.arachnoserver.org/toxincard.html?id=%s
Example ArachnoServer ID | AS000014
CCmisc BMC Genomics 10:375-375(2009); [Pubmed: 19674480]
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EMBOSS Data Types
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Sequences
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Features
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Attached to sequences
Independent data objects
Bio-Ontologies (OBO)
Taxonomy (NCBI)
Data Resources
Assembled reads
Text
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Nucleotide (DNA and RNA)
Protein
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Text, HTML, XML
EMBOSS Datatypes
New data types
• Reuse “USA” syntax
• [Server:] Dbname : identifier
Database has an access method
• [Server:] Dbname – field : query General field names
• Data types: features, bio-ontologies, taxonomy, etc.
• Access methods: HTTP, DAS, BioMart, Ensembl, ...
• Multiple types and formats for a server/resource
• type: “sequence features”
• format: “embl fasta”
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EMBOSS Query Language
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Query fields are now made general
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Multiple queries combined
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Any field queriable by the access method (DAS, SRS, …)
Any index created by indexing applications
Any query term in the data resource catalogue
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For one data resource
AND, OR, … to combine queries
EMBOSS as a DAS Client
DAS Server Definitions
SERVER das [
method: "dassource"
type:
"sequence, features"
url:
"http://www.dasregistry.org/das/"
comment: "access sequence/feature sources listed on das registry
(http://www.dasregistry.org/das/)"
cachefile: "server.dassource"
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DAS Server Definitions
SERVER ensembldas [
method: "dassource"
type:
"sequence, features"
url:
"http://www.ensembl.org/das/"
comment: "access sequence/feature sources on ensembl das server
(http://www.ensembl.org/das/)"
cachefile: "server.ensembldas"
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DAS Example
DB Ensembl_Human_Genes [
method: das
type: "Sequence, Features“
taxon: "9606“
format: "das, dasgff“
url: http://www.ebi.ac.uk/das-srv/genedas/das/
Homo_sapiens.Gene_ID.reference
example: "ENSG00000139618“
comment: "The Ensembl human Gene_ID reference source, serving
sequences and non-location features.“
hasaccession: "N“
identifier: "segment“
fields: "segment, type, category, categorize, feature_id“
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Ensembl DAS Example
DB Felis_catus_CAT_prediction_transcript [
method: das
type: "Nucfeatures“
taxon: "9685“
format: "dasgff“
url: http://www.ensembl.org/das/Felis_catus.CAT.prediction_transcript
example: "scaffold_209987[1:550]“
comment: "Annotation source for Felis_catus prediction_transcript“
hasaccession: "N“
identifier: "segment“
fields: "segment, type, category, categorize, feature_id“
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EMBOSS Query Language
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das: ensembl_human_genes: ENSG00000139618
ensembldas: Felis_catus_CAT_prediction_transcript:
scaffold_209987 [1:550]
das: Homo_sapiens_GRCh37_transcript: 10
[32889611:32973347]
das: uniprot: P00280
das: cath: 5pti
das: uniparc: UPI000000000A
das: Homo_sapiens_GRCh37_reference{segment: 11 & type: supercontig}
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EMBOSS Query Language: Future
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Ontology-based searches of data resources
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Search for applications matching data types
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Taxonomy
EDAM terms
• Resources
• Data types
• Identifiers
Descriptions
Sequences and features
Nucleotide and protein
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Support for DAS advanced query ...
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Acknowledgements
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EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag, Martin Senger, Tom Oinn, Jaina Mistry,
Rodrigo Lopez, Sharmilla Pillai, Hamish McWilliam
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RFCGR/HGMP: Alan Bleasby, Jon Ison, Tim Carver, Hugh Morgan, Claude Beazley, Lisa Mullan,
Damian Counsell, Gary Williams, Val Curwen, Mark Faller, Sinead O’Leary, Thon deBoer, Martin
Bishop
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Sanger Institute: Ian Longden, Richard Bruskiewich, Simon Kelley
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LION: Mahmut Uludag, Thomas Laurent, Bijay Jassal, Bren Vaughan, Thure Etzold
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National bioinformatics service providers in: Norway, Spain, Italy, Netherlands, Germany, Belgium,
Russia, China, Canada, Australia, Argentina
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Others: Catherine Letondal, Don Gilbert, Rodger Staden, Bill Pearson, Webb Miller, Marie-Laetitia
Denayer, Amandine Schurmann, Gabriele Weiler, Luke McCarthy, David Mathog, David Bauer,
Henrikki Almusa, Thomas Siegmund, Scott Markel, Darryl Leon, Bastien Chevreux, Ivo Hofacker, ...
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IBM, Hewlett-Packard, (Compaq), Apple, SGI, Sun, LION bioscience, SciTegic, Cambridge
University Press
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Open-Bio Foundation, Sourceforge, Debian, Fedora, CEH
... And the British Antarctic Survey
http://emboss.sourceforge.net
http://emboss.open-bio.org/wiki/Latest_developments
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