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Metadata

URI
http://biohackathon.org/resource/faldo
Version Information
Created at the Biohackathon 2012 and 2013
License
http://creativecommons.org/publicdomain/zero/1.0/
Ontology RDF
RDF (turtle)

Table of Contents

  1. Classes
  2. Object Properties
  3. Datatype Properties
  4. Namespaces
  5. Legend

Overview

Pictures say 1,000 words
Figure 1: Ontology overview

Classes

Bag of regionsc # Classes

URI http://biohackathon.org/resource/faldo#BagOfRegions
Description

Used to describe a location that consists of a number of Regions but where the order is not known. e.g. the oddly named order() keyword in a INSDC file.

Super-classes Collection of regionsc
rdf:Bagc

Both strands positionc # Classes

URI http://biohackathon.org/resource/faldo#BothStrandsPosition
Description

The 'both strands position' indicates a region that is best described as being on 'both' strands of a double-stranded sequence, rather than one or the other.

Super-classes Stranded positionc

C-Terminal positionc # Classes

URI http://biohackathon.org/resource/faldo#C-TerminalPosition
Description

The C-terminus is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH).

Super-classes Exact positionc

Collection of regionsc # Classes

URI http://biohackathon.org/resource/faldo#CollectionOfRegions
Description

Sometimes a location of a feature is defined by a collection of regions e.g. join() and order() in INSDC records. One should always try to model the semantics more accurately than this, these are fallback options to encode legacy data.

Super-classes owl:Thingc
Restrictions rdfs:member only (Regionc or Collection of regionsc)
Sub-classes Bag of regionsc
List of regionsc

Exact positionc # Classes

URI http://biohackathon.org/resource/faldo#ExactPosition
Description

A position that is exactly known.

Super-classes Positionc
Restrictions positiondp exactly 1
Sub-classes C-Terminal positionc
N-TerminalPositionc
In domain of positiondp
In range of afterop
beforeop

Forward/positive strand positionc # Classes

URI http://biohackathon.org/resource/faldo#ForwardStrandPosition
Description

The position is on the forward (positive, 5' to 3') strand. Shown as a '+' in GFF3 and GTF.

Super-classes Stranded positionc

Fuzzy positionc # Classes

URI http://biohackathon.org/resource/faldo#FuzzyPosition
Description

A position that lacks exact data.

Super-classes Positionc
Sub-classes One of positionsc
Indeterminate position within a rangec

In between positionsc # Classes

URI http://biohackathon.org/resource/faldo#InBetweenPosition
Description

This indicates that a feature is between two other positions that are both known exactly and that are next to each other. An example is a restriction enzyme cutting site. The cut is after one position and before the other position (hence, in between).

Super-classes Positionc
(n8fec3ec63b824b70b48282d14f4a6c08b9c and n8fec3ec63b824b70b48282d14f4a6c08b10c)
In domain of beforeop
afterop

Indeterminate position within a rangec # Classes

URI http://biohackathon.org/resource/faldo#InRangePosition
Description

Use when you have an idea of the range in which you can find the position, but you cannot be sure about the exact position.

Super-classes Fuzzy positionc
(n8fec3ec63b824b70b48282d14f4a6c08b14c and n8fec3ec63b824b70b48282d14f4a6c08b15c)

List of regionsc # Classes

URI http://biohackathon.org/resource/faldo#ListOfRegions
Description

As an ordered list of regions (but the list might not be complete).

Super-classes Collection of regionsc
rdf:Seqc

N-TerminalPositionc # Classes

URI http://biohackathon.org/resource/faldo#N-TerminalPosition
Description

The position of the starting amino-acid a protein or polypeptide terminated by an amino acid with a free amine group (-NH2). The convention for writing peptide sequences is to put the N-terminus on the left and write the sequence from N- to C-terminus. Instances of this class are often used when the reference sequence is not complete

Super-classes Exact positionc

One of positionsc # Classes

URI http://biohackathon.org/resource/faldo#OneOfPosition
Description

The position is known to be one of the more detailed positions listed by the location predicate.

Super-classes Fuzzy positionc

Positionc # Classes

URI http://biohackathon.org/resource/faldo#Position
Description

Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.

Super-classes owl:Thingc
Restrictions referenceop exactly 1
Sub-classes Stranded positionc
Fuzzy positionc
In between positionsc
Exact positionc
In range of beginop
endop

Regionc # Classes

URI http://biohackathon.org/resource/faldo#Region
Description

A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene.

Super-classes (n8fec3ec63b824b70b48282d14f4a6c08b20c and n8fec3ec63b824b70b48282d14f4a6c08b21c)
owl:Thingc

Negative/reverse strand positionc # Classes

URI http://biohackathon.org/resource/faldo#ReverseStrandPosition
Description

The position is on the reverse (complement, 3' to 5') strand of the sequence. Shown as '-' in GTF and GFF3.

Super-classes Stranded positionc

Stranded positionc # Classes

URI http://biohackathon.org/resource/faldo#StrandedPosition
Description

Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'.

Super-classes Positionc
Sub-classes Negative/reverse strand positionc
Both strands positionc
Forward/positive strand positionc

Object Properties

afterop # OPs

URI http://biohackathon.org/resource/faldo#after
Description

This predicate is used when you want to describe a non-inclusive range. Only used in the InBetweenPosition to say it is after a nucleotide, but before the next one.

Domain(s) In between positionsc
Range(s) http://biohackathon.org/resource/faldo#ExactPositionc

beforeop # OPs

URI http://biohackathon.org/resource/faldo#before
Description

This predicate is used to indicate that the feature is found before the exact position. Use to indicate, for example, a cleavage site. The cleavage happens between two amino acids before one and after the other.

Domain(s) In between positionsc
Range(s) http://biohackathon.org/resource/faldo#ExactPositionc

beginop # OPs

URI http://biohackathon.org/resource/faldo#begin
Description

The inclusive beginning of a position. Also known as start.

Inverse properties beginOfop
Domain(s) (Regionc or Indeterminate position within a rangec)
Range(s) http://biohackathon.org/resource/faldo#Positionc

beginOfop # OPs

URI http://biohackathon.org/resource/faldo#beginOf
Description

This is the inverse of the begin:property. It is included to make it easier to write a number of OWL axioms. You should rarely use this in your raw data.

Inverse properties beginop

endop # OPs

URI http://biohackathon.org/resource/faldo#end
Description

The inclusive end of the position.

Inverse properties endOfop
Range(s) http://biohackathon.org/resource/faldo#Positionc

endOfop # OPs

URI http://biohackathon.org/resource/faldo#endOf
Description

This is the inverse of the begin:end. It is included to make it easier to write a number of OWL axioms. You should rarely use this in your raw data.

Inverse properties endop

locationop # OPs

URI http://biohackathon.org/resource/faldo#location
Description

This is the link between the concept whose location you are annotating and its range or position. For example, when annotating the region that describes an exon, the exon would be the subject and the region would be the object of the triple or: 'active site' 'location' [is] 'position 3'.

Range(s) http://biohackathon.org/resource/faldo#CollectionOfRegions http://biohackathon.org/resource/faldo#Region http://biohackathon.org/resource/faldo#Position

possiblePositionop # OPs

URI http://biohackathon.org/resource/faldo#possiblePosition
Description

One of the possible positions listed for a OneOfPosition element.

referenceop # OPs

URI http://biohackathon.org/resource/faldo#reference
Description

The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly.

Datatype Properties

positiondp # DPs

URI http://biohackathon.org/resource/faldo#position
Description

Denoted in 1-based closed coordinates, i.e. the position on the first amino acid or nucleotide of a sequence has the value 1. For nucleotide sequences we count from the 5'end of the sequence, while for Aminoacid sequences we start counting from the N-Terminus.

Domain(s) Exact positionc

Namespaces

default (:)
http://biohackathon.org/resource/faldo
dct
http://purl.org/dc/terms/
owl
http://www.w3.org/2002/07/owl#
prov
http://www.w3.org/ns/prov#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
sdo
http://schema.org/
skos
http://www.w3.org/2004/02/skos/core#
spin
http://spinrdf.org/spin#
wiki
http://en.wikipedia.org/wiki/
xsd
http://www.w3.org/2001/XMLSchema#

Legend

cClasses
opObject Properties
fpFunctional Properties
dpData Properties
dpAnnotation Properties
pProperties
niNamed Individuals