"Mickael Silva"
João Carriço
NGSOnto
OWL
This ontology aims to describe and anotate all pipelines of a NGS process, starting from DNA extraction from an isolate to the assembled draft genome, allowing the reproducibility of the processes. nConstructed from BFO (Basic Formal Ontology), an upper level ontology (http://www.ifomis.org/bfo) and designed based on NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) and EMBL-EBI European Nucleotide Archive (http://www.ebi.ac.uk/ena/) public data.
Belong To
Sequenced on
used Parameter
used Software
used function
execute
has protocol
has step
has workflow
adaptor
ammount DNA
buffer
configuration file
end repair enzyme
extraction method
file
file extension
fragmentation method
library type
name
minimum length of the fragments to be selected on the filtering process
parameter designation
parameter value
range of fragments size
reference genome
scaffolding
script file
script language
sequence coverage
size selector
software version
start date
strategy
study description
study title
study type
tailing
uri
version
date
index
DNA Extraction kit name
Parameter
"Typically a simple numerical or string value that controls the operation of a tool." [http://edamontology.org]nnhttp://edamontology.org/data_2527
1
1
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.nnhttp://purl.obolibrary.org/obo/IAO_0000010
1
1
A manual script is string or file whose instructions can be executed using a software interpreter.
Library
Collection of the 5' and 3' ends of DNA or cDNA fragments. Represents the output of a Library Preparation process.
Processed Reads
Reads that have suffered some processing.
Raw Reads
Raw output of a Sequencing Process.
Next Generation Sequencing Process
1
1
1
A single process execution that may occur within a NGS pipeline.
Data processing
Filtering
Message
A result output of a single process. This output may be an input for another process .
Data Processing protocol
1
1
Sequence cutting protocol
Filtering protocol
Resource that provides access to software, applications, or toolkits that perform alter the spatial-temporal spectral content of data.nnhttp://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Filtering
DNA Extraction Protocol
1
Library Preparation Protocol
1
1
1
1
1
1
Sequence assembly protocol
1
1
1
Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.nnhttp://edamontology.org/operation_0310
de-novo assembly protocol
1
1
mapping assembly protocol
sequencing protocol
1
Step
1
Execution step
1
NGS Workflow step
1
1
1
1
1
pipeline
1
1
1
1
1
1
1
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.nntnnhttp://purl.obolibrary.org/obo/OBI_0400103
1
1
A set of overlapping DNA segments that together represent a consensus region of DNA. Represents the output of a De-novo assembly process
1
A string or a file that contains a nucleotid sequence representing that read.