gene
type: Class
subclass of: region
comment: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. (source: Sequence Ontology)

has input value
type: ObjectProperty
comment: This property links a process to all its input value. The input values belong to only data_collection (parameter values are linked to process by property has_parameter).
domain: process
sub property of: has participant
range: peo resource:arc02cfb1

has output value
type: ObjectProperty
comment: This property links a process to all its output value. The output values belong to only data_collection (parameter values are linked to process by property has_parameter).
domain: process
sub property of: has participant
range: peo resource:arc02cfb4

region
type: Class
subclass of: domain parameter
comment: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids (source: Sequence Ontology).

is allele of
type: ObjectProperty
comment: If two paralogous genes occur in the same gene, they are alleles
sub property of: is paralogous to

PLO:000003
type: Class
subclass of: domain parameter
comment: a variant of an organism, or an inbred organism used for experimental purposes

COG info
type: Class
subclass of: researcher note
comment: The set of genes in Leishmania major and T. brucei, if any, that are orthologous to a given T. cruzi gene.

DBchangelog
type: Class
subclass of: technician note
comment: Automatically produced log of any changes that are made in the database, including the date they were made and the name of the person who made them.

GO term
type: Class
subclass of: data collection
comment: A node in an ontological tree. Can refer to biological process, cellular component, or molecular function.

KOlog
type: Class
subclass of: experiment justification
comment: Log of what has been done to date in the production of KO plasmids for a given KO target.

SAM result
type: Class
subclass of: data collection
comment: The significance, or not, of the degree of gene expression regulation for a gene as determined from microarray analysis using SAM analysis, which is a statistical test for significance.

Tcruzi lifecyclestage subsample
type: Class
subclass of: sample
subclass of: peo resource:arc02cfb7
comment: Growth of specific lifecycle stage of Trypanosoma cruzi.

Tcruzi sample
type: Class
subclass of: sample
comment: Trypanosoma cruzi cells in growth medium

accession number
type: Class
subclass of: domain parameter
comment: An unique identifier given to a DNA or protein sequence record.

allele designation
type: Class
subclass of: laboratory experiment parameters
comment: For diploid (or polyploid) organisms where a knockout construct plasmid is created for each allele of a gene, the allele_designation is the assignment of allele number for a particular knockout plasmid.

allele ko log
type: Class
subclass of: researcher note
comment: Log of what has been done to date in the production of a KO plasmid for a given KO target for a specific allele of that target gene.

assembly confidence notes
type: Class
subclass of: experiment notes
comment: Description of the likelihood that the published and assembled sequence for a given locus in the genome is correct.

cell cloning
type: Class
subclass of: strain creation process
subclass of: peo resource:arc02cfb8
subclass of: peo resource:arc02cfb9
subclass of: peo resource:arc02cfb10
subclass of: peo resource:arc02cfb11
comment: Selection to produce a population of genetically-identical individuals

chr allele note
type: Class
subclass of: researcher note
comment: Description of the alleles of a target gene regarding whether T. cruzi is heterozygous or homozygous for the gene and/or if there are any interruptions in the allele(s) for a gene resulting from possible gaps in the published sequence.

cloned sample
type: Class
subclass of: Tcruzi sample
comment: A sample of cells that has been grown from a single starter cell.

cloned sample designate
type: Class
subclass of: cloned sample
comment: A cloned_sample_designate is the instance of cloned_sample that is chosen by a researcher to be the clone of a particular strain that should be used for subsequent experiments involving that strain.

culture medium
type: Class
subclass of: domain parameter
comment: Liquid broth designed to support the growth of microorganisms. Contains a mixture of essential nutrients, as well as nutrients designed to optimise growth.

culture parameter
type: Class
subclass of: domain parameter
comment: An aspect of the culture that defines certain characteristics of an experiment.

data source
type: Class
subclass of: agent
comment: A platform, such as microarrays (transcriptome) or mass spectrometry (proteome), used for generating data.

drug
type: Class
subclass of: domain parameter
comment: Any chemical substance that, when absorbed into a cell, alters normal cell function

drug attribute
type: Class
subclass of: domain parameter
comment: Attributes of the specified drug.

drug concentration
type: Class
subclass of: drug attribute
comment: Concentration of drug used in experiment.

drug resistant plasmid
type: Class
subclass of: plasmid
comment: A plasmid that is used to introduce and express a specific drug resistant gene into a target cell

plasmid
type: Class
subclass of: data collection
comment: an extra-chromosomal DNA molecule separate from the chromosomal DNA which is capable of replicating independently of the chromosomal DNA - normally circular and double stranded. Often referred to as a vector in molecular biology.

drug selected sample
type: Class
subclass of: Tcruzi sample
comment: A sample that has been grown under selective drug pressure, that is, in the presence of a normally lethal compound.

drug selection
type: Class
subclass of: strain creation process
subclass of: peo resource:arc02cfb12
subclass of: peo resource:arc02cfb13
subclass of: peo resource:arc02cfb14
subclass of: peo resource:arc02cfb15
subclass of: peo resource:arc02cfb16
comment: The presence of a drug used to put selective pressure on cells which are expressing a protein conferring resistance against that drug.

experiment justification
type: Class
subclass of: experiment notes
comment: The justification for performing a particular experiment.

experiment notes
type: Class
subclass of: laboratory experiment parameters
comment: Any notes made by a researcher for the design, tracking, and results of experiments

five prime intergenic forward region
type: Class
subclass of: five prime intergenic region
comment: Forward strand of the double stranded DNA sequence for a five prime intergenic region.

five prime intergenic region
type: Class
subclass of: intergenic region
comment: DNA sequence between the gene upstream of a target gene and the target gene.

intergenic region
type: Class
subclass of: region
comment: The region between two known genes (source: Sequence Ontology).

five prime intergenic reverse region
type: Class
subclass of: five prime intergenic region
comment: Reverse strand of the double stranded DNA sequence for a five prime intergenic region.

five prime primer
type: Class
subclass of: primer
comment: As above, in the special case of primers used to amplify a target sequence that is in the 5’ flanking sequence to a gene of interest for gene knockout.

five prime reverse primer
type: Class
subclass of: five prime primer
comment: A five prime primer used to amplify the reverse strand of the 5’ flanking sequence to a gene of interest for gene knockout.

freezer
type: Class
subclass of: agent
comment: A freezer is a dry, cold-storage machine.

freezer location
type: Class
subclass of: spatial parameter
comment: Where freezer is located.

gene knockout process
type: Class
subclass of: process
subclass of: peo resource:arc02cfb20
comment: The method by which a gene knock out is produced

group number
type: Class
subclass of: laboratory experiment parameters
comment: Sequential number assigned to groups of genes that are taken through the KO process together. Begins with their primers being designed and ordered together.

hybridization
type: Class
subclass of: transcriptome process
comment: A labelled cDNA probe is incubated with the microarray.

kinetoplast position
type: Class
subclass of: spatial parameter
comment: Position of the kinetoplast in relation to the nucleus.

knockout construct plasmid
type: Class
subclass of: plasmid
comment: A plasmid that is used to introduce and express a specific drug resistant gene into a target cell, whilst disrupting or deleting a native gene

knockout plasmid
type: Class
subclass of: agent
comment: A plasmid that is used to introduce and express a specific drug resistant gene into a target cell, whilst disrupting or deleting a native gene

knockout plasmid construction
type: Class
subclass of: plasmid construction
subclass of: peo resource:arc02cfb21
subclass of: peo resource:arc02cfb25
subclass of: peo resource:arc02cfb26
subclass of: peo resource:arc02cfb31
comment: The process of taking one or more plasmids containing drug resistance and target region sequences and creating a knockout plasmid.

knockout project protocol
type: Class
subclass of: gene knockout process
comment: The top-level protocol by which a target gene is knocked-out from an organism.

knockout region construct protocol
type: Class
subclass of: gene knockout process
subclass of: peo resource:arc02cfb32
subclass of: peo resource:arc02cfb33
comment: The method by which a specific allele of a gene is knocked-out.

labelling
type: Class
subclass of: transcriptome process
comment: a cDNA probe is labelled with a radioactive marker.

laboratory experiment parameters
type: Class
subclass of: domain parameter
comment: Any parameters used by researchers to describe or track the progress of experiments that are specific to a particular lab's protocols.

log base2 ratio
type: Class
subclass of: statistical measure
comment: The log, base 2, of the signal intensity in channel 1 vs channel 2 for a microarray probe in a two-color hybridization.

microarray ANOVA cluster
type: Class
subclass of: laboratory experiment parameters
comment: Cluster of significant genes that were identified using ANOVA.

microarray plate reader
type: Class
subclass of: agent
comment: A machine that scans a microarray, reading the fluorescent signal intensity

nucleic acid
type: Class
subclass of: domain parameter
comment: A macromolecule composed of chains of monomeric nucleotides

oligo to gene assignment
type: Class
subclass of: transcriptome process
comment: This is a computational process to assign a given oligonucleotide to set of target genes

pathway
type: Class
subclass of: data collection
comment: The input and output molecules and the set of gene products that are associated with each other in that the gene products take the input molecule(s) and convert it to the output molecule(s), usually in a multistep process with each step being carried out by a different gene product(s). Similar to BioPax concept pathway. Biopax class was not re-used since there is no defined mapping between the BioPax class and Pathway ontology classes

peptide count
type: Class
subclass of: data collection
comment: The sum of the spectral counts for peptides hitting a particular gene or protein group.

phenotype
type: Class
subclass of: data collection
comment: Any observable characteristic or trait of an organism

plasmid construction
type: Class
subclass of: process
subclass of: peo resource:arc02cfb38
subclass of: peo resource:arc02cfb39
subclass of: peo resource:arc02cfb40
subclass of: peo resource:arc02cfb41
comment: The process by which a plasmid is made

plasmid construction step
type: Class
subclass of: status
comment: The step in the plasmid cloning process we are currently at.

polymerase chain reaction
type: Class
subclass of: process
comment: A technique for amplifying DNA sequences in vitro by separating the DNA into two strands and incubating it with oligonucleotide primers and DNA polymerase.

prehybridization
type: Class
subclass of: transcriptome process
comment: Incubation of microarray used to block nonspecific binding sites.

prime forward primer
type: Class
subclass of: five prime primer
comment: A five prime primer used to amplify the forward strand of the 5’ flanking sequence to a gene of interest for gene knockout.

primer
type: Class
subclass of: domain parameter
comment: An oligonucleotide used to initiate production of the reverse complement of a single stranded or denatured double stranded nucleic acid template by means of polymerase(s). Requires that the primer be complementary to the template.

priority
type: Class
subclass of: laboratory experiment parameters
comment: Assuming many genes that could be targeted for knockout, the priority is used to order when the particular genes are targeted.

protein group number
type: Class
subclass of: data collection
comment: Arbitrary number assigned to a protein group.

proteome analysis
type: Class
subclass of: process
subclass of: peo resource:arc02cfb42
subclass of: peo resource:arc02cfb43
subclass of: peo resource:arc02cfb44
subclass of: peo resource:arc02cfb45
subclass of: peo resource:arc02cfb46
subclass of: peo resource:arc02cfb47
subclass of: peo resource:arc02cfb48
subclass of: peo resource:arc02cfb49
subclass of: peo resource:arc02cfb50
comment: Analysis of proteome; i.e., all the proteins expressed by an organism.

peo resource:arc02cfb43
type: Restriction
on property: has output value
on class: standard deviation
max qualified cardinality: 2

peo resource:arc02cfb49
type: Restriction
on property: has output value
on class: Probability
max qualified cardinality: 2

Probability
type: Class
subclass of: statistical measure
comment: A statistical way of expressing knowledge or belief that an event will occur or has occurred.

purity
type: Class
subclass of: domain parameter
comment: The purity of the organism of interest in a complex sample which may contain media, contaminants, and other components

researcher
type: Class
subclass of: agent
comment: A researcher is any individual involved in the experimental processes.

researcher note
type: Class
subclass of: experiment notes
comment: Notes from researchers designing the experiment (renamed Other Notes)

sample
type: Class
subclass of: data collection
comment: An entity that is representative of a class, also known as a specimen.

sample characterization
type: Class
subclass of: gene knockout process
subclass of: peo resource:arc02cfb51
comment: The method by which a sample is characterized molecularly and phenotypically.

scanning
type: Class
subclass of: transcriptome process
comment: As done by microarray plate reader, reading the signal intensities of the microarray.

sequence coverage
type: Class
subclass of: drug selected sample
comment: The percent coverage for the protein based upon the matched peptide sequences (can be calculated) (source: Mass spectrometry Ontology).

sequence extraction
type: Class
subclass of: gene knockout process
subclass of: peo resource:arc02cfb52
subclass of: peo resource:arc02cfb59
comment: Copying a nucleotide or amino acid sequence from a database.

genome
type: Class
subclass of: domain parameter
comment: A genome is the sum of genetic material within a cell or virion (source: Sequence Ontology).

signal intensity
type: Class
subclass of: data collection
comment: Raw fluorescence intensity for spots on microarray following hybridisation.

spectral count
type: Class
subclass of: data collection
comment: The total number of time a given spectrum is detected in an MSMS run.

stage purity determination
type: Class
subclass of: process
subclass of: peo resource:arc02cfb60
subclass of: peo resource:arc02cfb61
subclass of: peo resource:arc02cfb62
subclass of: peo resource:arc02cfb63
comment: Process to determine purity of T. cruzi lifecycle sample.

PLO:000001
type: Class
subclass of: domain parameter
comment: Period of time in the lifecycle of a cell

standard deviation
type: Class
subclass of: statistical measure
comment: It is a standard deviation for biological replicates in microarray experiments.

statistical measure
type: Class
subclass of: data collection
comment: Different concepts or measures used in statistical analysis.

status
type: Class
subclass of: laboratory experiment parameters
comment: Status is an administrative parameter used to track the progress of experiments.

strain creation process
type: Class
subclass of: process
comment: The process by which a new strain of an organism is created via gene knockout.

strain creation protocol
type: Class
subclass of: strain creation process
subclass of: peo resource:arc02cfb64
subclass of: peo resource:arc02cfb70
comment: The protocol containing all sub-processes for strain creation.

strain summary
type: Class
subclass of: experiment notes
comment: Description of what has been done to date in the production of a given KO strain of T. cruzi. Begins with transfection of T. cruzi with KO plasmids.

subset
type: Class
subclass of: researcher note
comment: Group of genes in the list of target genes for KO that share common features, such as orthology or predicted function.

target region plasmid
type: Class
subclass of: plasmid
comment: A plasmid that contains some portion of the sequence of a gene targeted for genetic manipulation.

technician note
type: Class
subclass of: experiment notes
comment: Notes from the researchers performing the experiment in the lab (renamed KO Log)

temperature condition
type: Class
subclass of: culture parameter
comment: Temperature at which experiment is carried out. Usually measured on the Celsius scale.

three prime forward primer
type: Class
subclass of: three prime primer
comment: A three prime primer used to amplify the forward strand of the 3’ flanking sequence to a gene of interest for gene knockout.

three prime intergenic forward region
type: Class
subclass of: three prime intergenic region
comment: Forward strand of the double stranded DNA sequence for a three prime intergenic region.

three prime intergenic region
type: Class
subclass of: intergenic region
comment: DNA sequence between the gene downstream of a target gene and the target gene.

three prime intergenic reverse region
type: Class
subclass of: three prime intergenic region
comment: Reverse strand of the double stranded DNA sequence for a three prime intergenic region.

three prime primer
type: Class
subclass of: primer
comment: As above, in the special case of primers used to amplify a target sequence that is in the 3’ flanking sequence to a gene of interest for gene knockout.

three prime reverse primer
type: Class
subclass of: three prime primer
comment: A three prime primer used to amplify the reverse strand of the 3’ flanking sequence to a gene of interest for gene knockout.

transcriptome process
type: Class
subclass of: process
subclass of: peo resource:arc02cfb71
subclass of: peo resource:arc02cfb72
comment: The method by which a transcriptome experiment is carried out

microarray oligonucleotide
type: Class
subclass of: data collection
comment: Small DNA fragments (probes) chemically synthesized at specific locations (spots) on a microarray chip. Probes are typically 25-60 nucleotide long.

transfected genome
type: Class
subclass of: genome
comment: The genome of an organism after transfection of a plasmid into its genome.

transfected sample
type: Class
subclass of: Tcruzi sample
comment: T. cruzi sample that has been transfected with a plasmid

transfection buffer
type: Class
subclass of: domain parameter
comment: Buffer (or media) used during the transfection process.

transfection machine
type: Class
subclass of: agent
comment: Machine used to transfect cells with plasmid DNA, often by electroporation.

troubleshooting
type: Class
subclass of: technician note
comment: A yes or no designation regarding whether or not the construction of a given KO plasmid is currently undergoing troubleshooting due to difficulties in cloning.

Gene Function
type: Class
subclass of: domain parameter
comment: A term that expresses the function of a gene product (source: NCI Thesaurus).

Microarray Analysis
type: Class
subclass of: transcriptome process
subclass of: peo resource:arc02cfb82
subclass of: peo resource:arc02cfb83
subclass of: peo resource:arc02cfb84
subclass of: peo resource:arc02cfb85
subclass of: peo resource:arc02cfb86
subclass of: peo resource:arc02cfb87
comment: Analysis using microarray technology (e.g., cDNA arrays to see gene expression or protein microarrays to profile the pattern of proteins). (source: NCI Thesaurus)

PLO:000015
type: Class
subclass of: PLO:000005
comment: the nonflagellate intracellular morphologic stage in the development of Leishmania species parasites

PLO:000005
type: Class
subclass of: PLO:000001
comment: The nonflagellate intracellular morphologic stage in the development of trypanosomatid parasites

PLO:000017
type: Class
subclass of: PLO:000006
comment: the epimastigote stage of Trypanosoma brucei, found in the tsetse fly

PLO:000006
type: Class
subclass of: PLO:000001
comment: a developmental stage in trypanosomes. The undulating membrane is shortened and the flagellar pocket and the kinetoplast are anterior to the nucleus; in the previous stage they are near the tail and behind the nucleus. This stage occurs in the insect host.

PLO:000041
type: Class
subclass of: PLO:000027
comment: Infectious stage of Trypanosoma brucei, found in tsetse fly salivary glands.

PLO:000027
type: Class
subclass of: PLO:000008
comment: infectious stage of Trypanosoma species

PLO:000024
type: Class
subclass of: PLO:000008
comment: trypomastigote morphological form of Trypanosoma brucei

PLO:000008
type: Class
subclass of: PLO:000001
comment: the characteristic developmental stage of trypanosomes, a leaf-like form, with undulating membrane and flagellum.

PLO:000016
type: Class
subclass of: PLO:000005
comment: the nonflagellate intracellular morphologic stage in the development of Trypanosoma cruzi parasites

PLO:000018
type: Class
subclass of: PLO:000006
comment: the epimastigote stage of Trypanosoma cruzii, found in the insect vector

PLO:000042
type: Class
subclass of: PLO:000027
comment: Infectious stage of Trypanosoma cruzi, found in reduviid bug hindgut.

PLO:000025
type: Class
subclass of: PLO:000008
comment: trypomastigote morphological form of Trypanosoma cruzi

PLO:000026
type: Class
subclass of: PLO:000008
comment: A trypomastigote found in the mammalian host blood stream.

PLO:000011
type: Class
subclass of: domain parameter
comment: An organism that hosts a parasite

PLO:000019
type: Class
subclass of: PLO:000007
comment: Infectious promastigote stage of Leishmania species

PLO:000007
type: Class
subclass of: PLO:000001
comment: one of the morphological stages in the development of Leishmania species, characterized by a free anterior flagellum and the kinetoplast at the anterior end of the body.

PLO:000002
type: Class
subclass of: domain parameter
comment: any living structure capable of growth and reproduction

PLO:000020
type: Class
subclass of: PLO:000007
comment: non-infective promastigote stage of Leishmania species, found in the insect vector

PLO:000028
type: Class
subclass of: PLO:000008
comment: dividing form of Trypanosoma brucei found in the tsetse fly midgut

classic metabolic pathway
type: Class
subclass of: pathway
comment: Pathway involved in normal homeostasis of an organism. The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics.

disease pathway
type: Class
subclass of: pathway
comment: Pathway involved in producing or responding to a disease state.

drug pathway
type: Class
subclass of: pathway
comment: Pathway involved in drug metabolism and/or resistance.

regulatory pathway
type: Class
subclass of: pathway
comment: Pathway involved in regulating other pathways or processes.

signaling pathway
type: Class
subclass of: pathway
comment: Pathway in which one cell or set of cells communicates with another cell or set of cells, producing a patterned response in the receiving cell(s) and/or the signaling cell(s).

chromosome
type: Class
subclass of: domain parameter
comment: Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (source: Sequence Ontology).

DateTimeDescription
type: Class
subclass of: temporal parameter
comment: Concept (imported from OWL Time ontology) to describe temporal entities.