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).
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).
If two paralogous genes occur in the same gene, they are alleles
The set of genes in Leishmania major and T. brucei, if any, that are orthologous to a given T. cruzi gene.
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.
A node in an ontological tree. Can refer to biological process, cellular component, or molecular function.
Log of what has been done to date in the production of KO plasmids for a given KO target.
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.
Growth of specific lifecycle stage of Trypanosoma cruzi.
Trypanosoma cruzi cells in growth medium
An unique identifier given to a DNA or protein sequence record.
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.
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.
Description of the likelihood that the published and assembled sequence for a given locus in the genome is correct.
Selection to produce a population of genetically-identical individuals
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.
A sample of cells that has been grown from a single starter cell.
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.
Liquid broth designed to support the growth of microorganisms. Contains a mixture of essential nutrients, as well as nutrients designed to optimise growth.
An aspect of the culture that defines certain characteristics of an experiment.
A platform, such as microarrays (transcriptome) or mass spectrometry (proteome), used for generating data.
Any chemical substance that, when absorbed into a cell, alters normal cell function
Concentration of drug used in experiment.
A plasmid that is used to introduce and express a specific drug resistant gene into a target cell
A sample that has been grown under selective drug pressure, that is, in the presence of a normally lethal compound.
The presence of a drug used to put selective pressure on cells which are expressing a protein conferring resistance against that drug.
The justification for performing a particular experiment.
Any notes made by a researcher for the design, tracking, and results of experiments
Forward strand of the double stranded DNA sequence for a five prime intergenic region.
DNA sequence between the gene upstream of a target gene and the target gene.
Reverse strand of the double stranded DNA sequence for a five prime intergenic region.
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.
A five prime primer used to amplify the reverse strand of the 5’ flanking sequence to a gene of interest for gene knockout.
A freezer is a dry, cold-storage machine.
The method by which a gene knock out is produced
Sequential number assigned to groups of genes that are taken through the KO process together. Begins with their primers being designed and ordered together.
A labelled cDNA probe is incubated with the microarray.
Position of the kinetoplast in relation to the nucleus.
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
The process of taking one or more plasmids containing drug resistance and target region sequences and creating a knockout plasmid.
The top-level protocol by which a target gene is knocked-out from an organism.
The method by which a specific allele of a gene is knocked-out.
a cDNA probe is labelled with a radioactive marker.
Any parameters used by researchers to describe or track the progress of experiments that are specific to a particular lab's protocols.
The log, base 2, of the signal intensity in channel 1 vs channel 2 for a microarray probe in a two-color hybridization.
Cluster of significant genes that were identified using ANOVA.
A machine that scans a microarray, reading the fluorescent signal intensity
A macromolecule composed of chains of monomeric nucleotides
This is a computational process to assign a given oligonucleotide to set of target genes
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
The sum of the spectral counts for peptides hitting a particular gene or protein group.
Any observable characteristic or trait of an organism
The step in the plasmid cloning process we are currently at.
A technique for amplifying DNA sequences in vitro by separating the DNA into two strands and incubating it with oligonucleotide primers and DNA polymerase.
Incubation of microarray used to block nonspecific binding sites.
A five prime primer used to amplify the forward strand of the 5’ flanking sequence to a gene of interest for gene knockout.
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.
Assuming many genes that could be targeted for knockout, the priority is used to order when the particular genes are targeted.
Arbitrary number assigned to a protein group.
Analysis of proteome; i.e., all the proteins expressed by an organism.
The purity of the organism of interest in a complex sample which may contain media, contaminants, and other components
A researcher is any individual involved in the experimental processes.
Notes from researchers designing the experiment (renamed Other Notes)
An entity that is representative of a class, also known as a specimen.
The method by which a sample is characterized molecularly and phenotypically.
As done by microarray plate reader, reading the signal intensities of the microarray.
The percent coverage for the protein based upon the matched peptide sequences (can be calculated) (source: Mass spectrometry Ontology).
Copying a nucleotide or amino acid sequence from a database.
Raw fluorescence intensity for spots on microarray following hybridisation.
The total number of time a given spectrum is detected in an MSMS run.
Process to determine purity of T. cruzi lifecycle sample.
It is a standard deviation for biological replicates in microarray experiments.
Different concepts or measures used in statistical analysis.
Status is an administrative parameter used to track the progress of experiments.
The process by which a new strain of an organism is created via gene knockout.
The protocol containing all sub-processes for strain creation.
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.
Group of genes in the list of target genes for KO that share common features, such as orthology or predicted function.
A plasmid that contains some portion of the sequence of a gene targeted for genetic manipulation.
Notes from the researchers performing the experiment in the lab (renamed KO Log)
Temperature at which experiment is carried out. Usually measured on the Celsius scale.
A three prime primer used to amplify the forward strand of the 3’ flanking sequence to a gene of interest for gene knockout.
Forward strand of the double stranded DNA sequence for a three prime intergenic region.
DNA sequence between the gene downstream of a target gene and the target gene.
Reverse strand of the double stranded DNA sequence for a three prime intergenic region.
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.
A three prime primer used to amplify the reverse strand of the 3’ flanking sequence to a gene of interest for gene knockout.
The method by which a transcriptome experiment is carried out
The genome of an organism after transfection of a plasmid into its genome.
T. cruzi sample that has been transfected with a plasmid
Buffer (or media) used during the transfection process.
Machine used to transfect cells with plasmid DNA, often by electroporation.
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.
A term that expresses the function of a gene product (source: NCI Thesaurus).
Analysis using microarray technology (e.g., cDNA arrays to see gene expression or protein microarrays to profile the pattern of proteins). (source: NCI Thesaurus)
A statistical way of expressing knowledge or belief that an event will occur or has occurred.
the nonflagellate intracellular morphologic stage in the development of Leishmania species parasites
the epimastigote stage of Trypanosoma brucei, found in the tsetse fly
Infectious stage of Trypanosoma brucei, found in tsetse fly salivary glands.
trypomastigote morphological form of Trypanosoma brucei
the nonflagellate intracellular morphologic stage in the development of Trypanosoma cruzi parasites
the epimastigote stage of Trypanosoma cruzii, found in the insect vector
Infectious stage of Trypanosoma cruzi, found in reduviid bug hindgut.
trypomastigote morphological form of Trypanosoma cruzi
The nonflagellate intracellular morphologic stage in the development of trypanosomatid parasites
A trypomastigote found in the mammalian host blood stream.
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.
Period of time in the lifecycle of a cell
Infectious promastigote stage of Leishmania species
any living structure capable of growth and reproduction
a variant of an organism, or an inbred organism used for experimental purposes
non-infective promastigote stage of Leishmania species, found in the insect vector
dividing form of Trypanosoma brucei found in the tsetse fly midgut
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.
the characteristic developmental stage of trypanosomes, a leaf-like form, with undulating membrane and flagellum.
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.
Pathway involved in producing or responding to a disease state.
Pathway involved in drug metabolism and/or resistance.
Pathway involved in regulating other pathways or processes.
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).
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).
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)
A genome is the sum of genetic material within a cell or virion (source: Sequence Ontology).
The region between two known genes (source: Sequence Ontology).
Small DNA fragments (probes) chemically synthesized at specific locations (spots) on a microarray chip. Probes are typically 25-60 nucleotide long.
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.
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).
Concept (imported from OWL Time ontology) to describe temporal entities.