IRI:
http://biohackathon.org/resource/faldo
Current version:
Created at the Biohackathon 2012 and 2013
Other visualisation:
Ontology source

Table of Content

  1. Classes
  2. Object Properties
  3. Data Properties
  4. Namespace Declarations

Classes

Bag of regionsc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#BagOfRegions

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.
has super-classes
Collection of regionsc
bagc

Both strands positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#BothStrandsPosition

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.
has super-classes
Stranded positionc
is disjoint with
Forward/positive strand positionc, Negative/reverse strand positionc

C-Terminal positionc back to ToC or Class ToC

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

The C-terminus is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH).
has super-classes
Exact positionc
is disjoint with
n terminal positionc

Collection of regionsc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#CollectionOfRegions

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.
has super-classes
thingc
memberop only Collection of regionsc or Regionc
has sub-classes
Bag of regionsc, List of regionsc

Exact positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ExactPosition

A position that is exactly known.
has super-classes
Positionc
positiondp exactly 1
has sub-classes
C-Terminal positionc, n terminal positionc
is in domain of
positiondp
is in range of
afterop, beforeop
has keys
referenceop , positiondp
is disjoint with
In between positionsc, Indeterminate position within a rangec, One of positionsc

Forward/positive strand positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ForwardStrandPosition

The position is on the forward (positive, 5' to 3') strand. Shown as a '+' in GFF3 and GTF.
has super-classes
Stranded positionc
is disjoint with
Both strands positionc, Negative/reverse strand positionc

Fuzzy positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#FuzzyPosition

A position that lacks exact data.
has super-classes
Positionc
has sub-classes
Indeterminate position within a rangec, One of positionsc

In between positionsc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#InBetweenPosition

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).
has super-classes
Positionc
(afterop exactly 1 Exact positionc) and (beforeop exactly 1 Exact positionc)
is in domain of
afterop, beforeop
is disjoint with
Exact positionc, Indeterminate position within a rangec, One of positionsc

Indeterminate position within a rangec back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#InRangePosition

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.
has super-classes
Fuzzy positionc
(beginop max 1 Positionc) and (endop max 1 Positionc)
is disjoint with
Exact positionc, In between positionsc, One of positionsc, Stranded positionc

List of regionsc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ListOfRegions

As an ordered list of regions (but the list might not be complete).
has super-classes
Collection of regionsc
seqc

n terminal positionc back to ToC or Class ToC

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

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
has super-classes
Exact positionc
is disjoint with
C-Terminal positionc

Negative/reverse strand positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ReverseStrandPosition

The position is on the reverse (complement, 3' to 5') strand of the sequence. Shown as '-' in GTF and GFF3.
has super-classes
Stranded positionc
is disjoint with
Both strands positionc, Forward/positive strand positionc

One of positionsc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#OneOfPosition

The position is known to be one of the more detailed positions listed by the location predicate.
has super-classes
Fuzzy positionc
is disjoint with
Exact positionc, In between positionsc, Indeterminate position within a rangec

Positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#Position

Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.
has super-classes
thingc
referenceop exactly 1
has sub-classes
Exact positionc, Fuzzy positionc, In between positionsc, Stranded positionc
is in range of
beginop, endop

Regionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#Region

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.
has super-classes
thingc
(beginop exactly 1 Positionc) and (endop exactly 1 Positionc)
has keys
beginop , endop

Stranded positionc back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#StrandedPosition

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'.
has super-classes
Positionc
has sub-classes
Both strands positionc, Forward/positive strand positionc, Negative/reverse strand positionc
is disjoint with
Indeterminate position within a rangec

Object Properties

afterop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#after

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.
has domain
In between positionsc
has range
Exact positionc

beforeop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#before

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.
has domain
In between positionsc
has range
Exact positionc

beginop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#begin

The inclusive beginning of a position. Also known as start.
has domain
Indeterminate position within a rangec or Regionc
has range
Positionc
is inverse of
beginOfop

beginOfop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#beginOf

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.
is inverse of
beginop

endop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#end

The inclusive end of the position.
has range
Positionc
is inverse of
endOfop

endOfop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#endOf

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.
is inverse of
endop

locationop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#location

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'.
has range
Collection of regionsc or Positionc or Regionc

possiblePositionop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#possiblePosition

One of the possible positions listed for a OneOfPosition element.

referenceop back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#reference

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

Data Properties

positiondp back to ToC or Data Property ToC

IRI: http://biohackathon.org/resource/faldo#position

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.
has domain
Exact positionc
has range

Namespace Declarations back to ToC

default namespace
http://biohackathon.org/resource/faldo#
files
http://www.insdc.org/files/
owl
http://www.w3.org/2002/07/owl#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
resource
http://biohackathon.org/resource/
spin
http://spinrdf.org/spin#
terms
http://purl.org/dc/terms/
wiki
http://en.wikipedia.org/wiki/
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.