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 COG_info The set of genes in Leishmania major and T. brucei, if any, that are orthologous to a given T. cruzi gene. DBchangelog 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. DateCompleted DateOfLastModification DateStarted GO_term A node in an ontological tree. Can refer to biological process, cellular component, or molecular function. KOlog Log of what has been done to date in the production of KO plasmids for a given KO target. SAM_result 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 Growth of specific lifecycle stage of Trypanosoma cruzi. Tcruzi_sample Trypanosoma cruzi cells in growth medium accession_number An unique identifier given to a DNA or protein sequence record. allele_designation 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 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 Description of the likelihood that the published and assembled sequence for a given locus in the genome is correct. cell_cloning Selection to produce a population of genetically-identical individuals chr_allele_note 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 A sample of cells that has been grown from a single starter cell. cloned_sample_designate 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 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 An aspect of the culture that defines certain characteristics of an experiment. data_source A platform, such as microarrays (transcriptome) or mass spectrometry (proteome), used for generating data. drug Any chemical substance that, when absorbed into a cell, alters normal cell function drug_attribute Attributes of the specified drug. drug_concentration Concentration of drug used in experiment. drug_resistant_plasmid A plasmid that is used to introduce and express a specific drug resistant gene into a target cell drug_selected_sample A sample that has been grown under selective drug pressure, that is, in the presence of a normally lethal compound. drug_selection The presence of a drug used to put selective pressure on cells which are expressing a protein conferring resistance against that drug. experiment_justification The justification for performing a particular experiment. experiment_notes Any notes made by a researcher for the design, tracking, and results of experiments five_prime_intergenic_forward_region Forward strand of the double stranded DNA sequence for a five prime intergenic region. five_prime_intergenic_region DNA sequence between the gene upstream of a target gene and the target gene. five_prime_intergenic_reverse_region Reverse strand of the double stranded DNA sequence for a five prime intergenic region. five_prime_primer 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 A five prime primer used to amplify the reverse strand of the 5’ flanking sequence to a gene of interest for gene knockout. freezer A freezer is a dry, cold-storage machine. freezer_location Where freezer is located. gene_knockout_process The method by which a gene knock out is produced group_number 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 A labelled cDNA probe is incubated with the microarray. kinetoplast_position Position of the kinetoplast in relation to the nucleus. knockout_construct_plasmid 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 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 The process of taking one or more plasmids containing drug resistance and target region sequences and creating a knockout plasmid. knockout_project_protocol The top-level protocol by which a target gene is knocked-out from an organism. knockout_region_construct_protocol The method by which a specific allele of a gene is knocked-out. labelling a cDNA probe is labelled with a radioactive marker. laboratory_experiment_parameters 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 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 Cluster of significant genes that were identified using ANOVA. microarray_plate_reader A machine that scans a microarray, reading the fluorescent signal intensity nucleic_acid A macromolecule composed of chains of monomeric nucleotides oligo_to_gene_assignment This is a computational process to assign a given oligonucleotide to set of target genes pathway 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 The sum of the spectral counts for peptides hitting a particular gene or protein group. phenotype Any observable characteristic or trait of an organism plasmid_construction The process by which a plasmid is made plasmid_construction_step The step in the plasmid cloning process we are currently at. polymerase_chain_reaction 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 Incubation of microarray used to block nonspecific binding sites. prime_forward_primer A five prime primer used to amplify the forward strand of the 5’ flanking sequence to a gene of interest for gene knockout. primer 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 Assuming many genes that could be targeted for knockout, the priority is used to order when the particular genes are targeted. protein_group_number Arbitrary number assigned to a protein group. 2 2 proteome_analysis Analysis of proteome; i.e., all the proteins expressed by an organism. purity The purity of the organism of interest in a complex sample which may contain media, contaminants, and other components researcher A researcher is any individual involved in the experimental processes. researcher_note Notes from researchers designing the experiment (renamed Other Notes) sample An entity that is representative of a class, also known as a specimen. sample_characterization The method by which a sample is characterized molecularly and phenotypically. scanning As done by microarray plate reader, reading the signal intensities of the microarray. sequence_coverage The percent coverage for the protein based upon the matched peptide sequences (can be calculated) (source: Mass spectrometry Ontology). sequence_extraction Copying a nucleotide or amino acid sequence from a database. signal_intensity Raw fluorescence intensity for spots on microarray following hybridisation. spectral_count The total number of time a given spectrum is detected in an MSMS run. stage_purity_determination Process to determine purity of T. cruzi lifecycle sample. standard_deviation It is a standard deviation for biological replicates in microarray experiments. statistical_measure Different concepts or measures used in statistical analysis. status Status is an administrative parameter used to track the progress of experiments. strain_creation_process The process by which a new strain of an organism is created via gene knockout. strain_creation_protocol The protocol containing all sub-processes for strain creation. strain_summary 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 Group of genes in the list of target genes for KO that share common features, such as orthology or predicted function. target_region_plasmid A plasmid that contains some portion of the sequence of a gene targeted for genetic manipulation. technician_note Notes from the researchers performing the experiment in the lab (renamed KO Log) temperature_condition Temperature at which experiment is carried out. Usually measured on the Celsius scale. three_prime_forward_primer 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 Forward strand of the double stranded DNA sequence for a three prime intergenic region. three_prime_intergenic_region DNA sequence between the gene downstream of a target gene and the target gene. three_prime_intergenic_reverse_region Reverse strand of the double stranded DNA sequence for a three prime intergenic region. three_prime_primer 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 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 The method by which a transcriptome experiment is carried out transfected_genome The genome of an organism after transfection of a plasmid into its genome. transfected_sample T. cruzi sample that has been transfected with a plasmid transfection_buffer Buffer (or media) used during the transfection process. transfection_machine Machine used to transfect cells with plasmid DNA, often by electroporation. troubleshooting 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. provenir:agent provenir:data_collection provenir:domain_parameter provenir:parameter provenir:process provenir:spatial_parameter provenir:temporal_parameter Thesaurus:Gene_Function A term that expresses the function of a gene product (source: NCI Thesaurus). Thesaurus:Microarray_Analysis Analysis using microarray technology (e.g., cDNA arrays to see gene expression or protein microarrays to profile the pattern of proteins). (source: NCI Thesaurus) Thesaurus:Probability A statistical way of expressing knowledge or belief that an event will occur or has occurred. ParasiteLifecycle:Leishmania_sp_amastigote the nonflagellate intracellular morphologic stage in the development of Leishmania species parasites PLO:000015 ParasiteLifecycle:Trypanosoma_brucei_epimastigote the epimastigote stage of Trypanosoma brucei, found in the tsetse fly PLO:000017 ParasiteLifecycle:Trypanosoma_brucei_metacyclic_trypomastigote Infectious stage of Trypanosoma brucei, found in tsetse fly salivary glands. PLO:000041 ParasiteLifecycle:Trypanosoma_brucei_trypomastigote trypomastigote morphological form of Trypanosoma brucei PLO:000024 ParasiteLifecycle:Trypanosoma_cruzi_amastigote the nonflagellate intracellular morphologic stage in the development of Trypanosoma cruzi parasites PLO:000016 ParasiteLifecycle:Trypanosoma_cruzi_epimastigote the epimastigote stage of Trypanosoma cruzii, found in the insect vector PLO:000018 ParasiteLifecycle:Trypanosoma_cruzi_metacyclic_trypomastigote Infectious stage of Trypanosoma cruzi, found in reduviid bug hindgut. PLO:000042 ParasiteLifecycle:Trypanosoma_cruzi_trypomastigote trypomastigote morphological form of Trypanosoma cruzi PLO:000025 ParasiteLifecycle:amastigote The nonflagellate intracellular morphologic stage in the development of trypanosomatid parasites PLO:000005 ParasiteLifecycle:blood_stream_form_trypomastigote A trypomastigote found in the mammalian host blood stream. PLO:000026 ParasiteLifecycle:epimastigote 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:000006 ParasiteLifecycle:host_organism An organism that hosts a parasite PLO:000011 ParasiteLifecycle:lifecycle_stage Period of time in the lifecycle of a cell PLO:000001 ParasiteLifecycle:metacyclic_promastigote Infectious promastigote stage of Leishmania species PLO:000019 ParasiteLifecycle:metacyclic_trypomastigote infectious stage of Trypanosoma species PLO:000027 ParasiteLifecycle:organism any living structure capable of growth and reproduction PLO:000002 ParasiteLifecycle:organism_strain a variant of an organism, or an inbred organism used for experimental purposes PLO:000003 ParasiteLifecycle:procyclic_promastigote non-infective promastigote stage of Leishmania species, found in the insect vector PLO:000020 ParasiteLifecycle:procyclic_trypomastigote dividing form of Trypanosoma brucei found in the tsetse fly midgut PLO:000028 ParasiteLifecycle:promastigote 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:000007 ParasiteLifecycle:trypomastigote the characteristic developmental stage of trypanosomes, a leaf-like form, with undulating membrane and flagellum. PLO:000008 PW:classic_metabolic_pathway 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. PW:disease_pathway Pathway involved in producing or responding to a disease state. PW:drug_pathway Pathway involved in drug metabolism and/or resistance. PW:regulatory_pathway Pathway involved in regulating other pathways or processes. PW:signaling_pathway 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). sequence:chromosome 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). sequence:gene 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) sequence:genome A genome is the sum of genetic material within a cell or virion (source: Sequence Ontology). sequence:intergenic_region The region between two known genes (source: Sequence Ontology). sequence:microarray_oligonucleotide Small DNA fragments (probes) chemically synthesized at specific locations (spots) on a microarray chip. Probes are typically 25-60 nucleotide long. sequence:plasmid 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. sequence:region 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). owl:Thing time:DateTimeDescription Concept (imported from OWL Time ontology) to describe temporal entities. transfection