1.2 13:04:2021 14:52 OBO-Edit 2.3.1 microbial_phenotype select is_a closure siegele definition expand assertion to term replaced by never_in_taxon Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) Class: ?X DisjointWith: RO_0002162 some ?Y RO:0002161 external never_in_taxon never_in_taxon true true is opposite_of RO:0002604 is_opposite_of is_opposite_of quality true true BRAND NAME Involved_in FORMULA INN IUPAC NAME InChI InChIKey SMILES SO feature annotation Abnormal/normal slim Absent/present slim Attribute slim cell_quality Disposition slim Grouping classes that can be excluded Aspergillus GO slim Candida GO slim Generic GO slim GOA and proteome slim Metagenomics GO slim PIR GO slim Plant GO slim Fission yeast GO slim Viral GO slim Yeast GO slim Prokaryotic GO subset Human phenotype slim Catalytic activity terms in need of attention Pathology slim Term not to be used for direct annotation Term not to be used for direct manual annotation Relational slim: types of quality that require an additional entity in order to exist Scalar slim Systematic synonym Value slim Viral overhaul terms subset_property synonym_type_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope in_subset shorthand part_of BFO:0000050 Example: amino_acid part_of polypeptide. Used in FYPO to identify phenotypes that are always observed in the context of another, usually larger-scale, phenotype. X part_of Y if X is a subregion of Y. part_of part_of sequence X part_of Y if X is a subregion of Y. http://precedings.nature.com/documents/3495/version/1 has_part BFO:0000051 Example: operon has_part gene. Inverse of part_of. Used in FYPO to link phenotypes that are collections of features to phenotypes representing the features. has_part has_part sequence Inverse of part_of. http://precedings.nature.com/documents/3495/version/1 preceded_by BFO:0000062 Used in FYPO when a phenotype is observed after another event, usually a GO biological process, has ended, and where there isn't a suitable process to use with a during relation. microbial_phenotype preceded_by preceded_by precedes BFO:0000063 Used in FYPO when a phenotype is observed before another event, usually a GO biological process, begins, and where there isn't a suitable process to use with a during relation. microbial_phenotype precedes precedes occurs in BFO:0000066 Used in FYPO to identify a location, usually a cellular component or cell type, within which a phenotype is observed or relevant. microbial_phenotype occurs_in occurs_in during GOREL:0000002 Identifies a process, cell cycle stage or life stage during which a phenotype is observed or relevant. during during microbial_phenotype exists_during GOREL:0000032 Identifies a process, cell cycle stage or life stage during which a phenotype that affects a continuant, such as a cellular component or the level of a substance, is observed or relevant. exists_during exists_during microbial_phenotype occurs_at GOREL:0000501 This relation is not constrained with respect to whether the place where an event occurs completely surrounds, or is adjacent to, the location indicated. Example: chromatin silencing at centromere unfolds_around centromere : Repression of transcription of centromeric DNA by the formation of heterochromatin. Used in FYPO to identify a position where a phenotype is observed or relevant, usually a DNA or RNA sequence feature specified by a SO ID. microbial_phenotype occurs_at occurs_at inheres_in RO:0000052 Used in FYPO as described in PATO best practices; identifies an entity that displays a quality in an entity-quality logical definition. Used only in logical definitions (aka xps). inheres_in inheres_in microbial_phenotype participates_in RO:0000056 external participates_in participates_in has role RO:0000087 chebi_ontology has_role has_role located in RO:0001025 Used in FYPO to indicate where a physical quality phenotype is observed. located_in located_in microbial_phenotype happens_during GOREL:0000001 Identifies a process, cell cycle stage or life stage during which a phenotype that affects an occurrent, i.e. a biological process or molecular function, is observed or relevant. RO:0002092 external happens_during happens_during ends_during RO:0002093 ends_during ends_during external regulates RO:0002211 external regulates regulates negatively regulates RO:0002212 external negatively_regulates negatively_regulates positively regulates RO:0002213 external positively_regulates positively_regulates has_output Def comes from gorel file. Used in FYPO where one phenotype (p) always results in an additional phenotype (c) as a consequence. There may be other ways to get phenotype (c). RO:0002234 has_output has_output microbial_phenotype p has output c if either: p has direct output c or p has output input c. Implies that if p happens, c always ensues. GOC:curators p has output c if either: p has direct output c or p has output input c. Implies that if p happens, c always ensues. inheres in part of RO:0002314 Used in FYPO as described in MP/HP logical definition best practices for processes, and in an analogous manner for cell/cell part structure; identifies an entity that displays a quality in an entity-quality logical definition. Used only in logical definitions (aka xps). inheres_in_part_of inheres_in_part_of microbial_phenotype output_of Inverse of has_output. Relation between a structure and a process that forms it, or between one process and a preceding process; A output_of B used where B has_output A isn't always true. Implies that process B is the only way to get output. Used in FYPO where one phenotype (c) always results when another phenotype (p) is present. Phenotype (p) may have other consequences in addition to phenotype (c). RO:0002353 formation results from microbial_phenotype output_of output_of PomBase:mah formation results from towards RO:0002503 Relation binding a relational quality or disposition to the relevant type of entity. Relation binding a relational quality or disposition to the relevant type of entity. Used in FYPO as described in PATO best practices; identifies abolished GO processes; identifies substances affected by phenotypes. quality towards towards adjacent_to A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap. adjacent_to sequence A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap. PMID:20226267 SO:ke contains 2010-10-14T01:32:15Z Example: pre_miRNA contains miRNA_loop. The inverse of contained_by. contains kareneilbeck sequence PMID:20226267 The inverse of contained_by. correlates_with correlates_with quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality PATOC:CJM q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. decreased_relative_to 2014-02-13T01:39:46Z Marcus P decreased_relative_to P' if and only if: given any process p that instantiates P under condition (genotype or environment) c, there is some process p' that instantiates P' under condition c', and P' is greater than P. decreased_relative_to microbial_phenotype true ECO:MCC P decreased_relative_to P' if and only if: given any process p that instantiates P under condition (genotype or environment) c, there is some process p' that instantiates P' under condition c', and P' is greater than P. derives_from derives_from sequence different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. directly_associated_with 2009-08-26T02:50:08Z Example: 'Lewy bodies increased number related to dystrophic neurite increased number' (from annotation of PMID:8740227 in http://ccdb.ucsd.edu/1.0/NDPO.owl#ndpo_404). Here the increase in the number of lewy bodies is directly_associated_with the increase in the number of dystrophic neurites. Association is weaker than correlation or proportionality. These relations may be later added to PATO. cjm directly_associated_with q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear. quality PATOC:cjm Wikipedia:Association_(statistics) q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear. has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section quality s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. has_dividend_entity has_dividend_entity quality has_dividend_quality has_dividend_quality quality has_divisor_entity has_divisor_entity quality has_divisor_quality has_divisor_quality quality has functional parent chebi_ontology has_functional_parent has_origin has_origin sequence has parent hydride chebi_ontology has_parent_hydride has_quality The relationship between a feature and an attribute. has_quality sequence has_ratio_quality has_ratio_quality quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality PATOC:CJM q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. increased_relative_to 2014-02-13T01:41:08Z Marcus P increased_relative_to P' if and only if: given any process p that instantiates P under condition (genotype or environment) c, there is some process p' that instantiates P' under condition c', and P' is less than P. increased_relative_to microbial_phenotype true ECO:MCC P increased_relative_to P' if and only if: given any process p that instantiates P under condition (genotype or environment) c, there is some process p' that instantiates P' under condition c', and P' is less than P. inversely_associated_with 2009-08-26T02:50:24Z Association is weaker than correlation or proportionality. These relations may be later added to PATO. cjm inversely_associated_with q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear. quality PATOC:cjm Wikipedia:Association_(statistics) q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear. is conjugate acid of chebi_ontology is_conjugate_acid_of true is conjugate base of chebi_ontology is_conjugate_base_of true is enantiomer of chebi_ontology is_enantiomer_of true is_magnitude_of is_magnitude_of pato.ontology is_measurement_of is_measurement_of pato.ontology is substituent group from chebi_ontology is_substituent_group_from is tautomer of chebi_ontology is_tautomer_of true is_unit_of is_unit_of pato.ontology member_of A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. member_of sequence non_functional_homolog_of A relationship between a pseudogenic feature and its functional ancestor. non_functional_homolog_of sequence A relationship between a pseudogenic feature and its functional ancestor. SO:ke overlaps 2010-10-14T01:33:15Z Example: coding_exon overlaps CDS. X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. kareneilbeck overlaps sequence PMID:20226267 X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. qualifier Used in FYPO as described in PATO best practices; placeholder relation to indicate normality/abnormality. microbial_phenotype qualifier realized_by quality realized_by reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. similar_in_magnitude_relative_to q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality similar_in_magnitude_relative_to PATOC:CJM q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. singly_occurring_form_of PATO divides qualities between normal (monadic, singly-occurring) qualities and relational qualities. Relational qualities stand in the 'towards' relation with respect to some additional entity. For example, The sensitivity of an eye towards red light. In some cases we want to represent a quality such as 'protruding' in both monadic and relational branches. We use this relation to link them. monadic_form_of quality singly_occurring_form_of transcribed_from 2009-08-19T12:05:39Z Example: primary_transcript transcribed_from gene. X is transcribed_from Y if X is synthesized from template Y. kareneilbeck sequence transcribed_from X is transcribed_from Y if X is synthesized from template Y. http://precedings.nature.com/documents/3495/version/1 transcribed_to 2009-08-19T12:08:24Z Example: gene transcribed_to primary_transcript. Inverse of transcribed_from. kareneilbeck sequence transcribed_to Inverse of transcribed_from. http://precedings.nature.com/documents/3495/version/1 variant_of A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A. Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith. sequence variant_of A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A. SO:immuno_workshop chemical entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. CHEBI:24431 chebi_ontology A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. CHEBI:Team biological role A role played by the molecular entity or part thereof within a biological context. CHEBI:24432 chebi_ontology A role played by the molecular entity or part thereof within a biological context. CHEBI:Team pesticide CHEBI:25944 Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests. Wikipedia:Pesticide chebi_ontology CHEBI:Team Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests. application CHEBI:33232 Intended use of the molecular entity or part thereof by humans. chebi_ontology CHEBI:Team Intended use of the molecular entity or part thereof by humans. antimicrobial agent A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:33281 antimicrobial chebi_ontology microbiocides A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:Team role A role is a particular behaviour which a material entity may exhibit. CHEBI:50906 chebi_ontology A role is a particular behaviour which a material entity may exhibit. CHEBI:Team reproduction GO:0000003 GO:0019952 GO:0050876 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. Wikipedia:Reproduction biological_process reproductive physiological process GOC:go_curators GOC:isa_complete GOC:jl ISBN:0198506732 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. cilium or flagellum-dependent cell motility Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella. GO:0001539 Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent, while the bacterial- and archaeal-type flagella have a different structure. The former are microtubule-based structures that lash back and forth and are present only in eukaryotes, while the latter achieve motility by rotation. Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. These three structures never co-exist in the same organism. Therefore, GO:0001539 'cilium or flagellum-dependent cell motility' is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term. Direct annotations to GO:0001539 'cilium or flagellum-dependent cell motility' may be amended during annotation QC. biological_process ciliary or bacterial-type flagellar motility ciliary/flagellar motility Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella. GOC:cilia GOC:hjd GOC:krc cellular_component GO:0005575 GO:0008372 NIF_Subcellular:sao1337158144 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. cellular component cellular_component subcellular entity NIF_Subcellular:nlx_subcell_100315 subcellular entity GOC:go_curators NIF_Subcellular:sao-1337158144 The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. cell GO:0005623 NIF_Subcellular:sao1813327414 The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. Wikipedia:Cell_(biology) cellular_component GOC:go_curators The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0006139 GO:0055134 biological_process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolism Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai GOC:dph GOC:tb nucleobase, nucleoside, nucleotide and nucleic acid metabolic process DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. DNA metabolism GO:0006259 GO:0055132 biological_process cellular DNA metabolism Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. ISBN:0198506732 DNA replication GO:0006260 GO:0055133 Reactome:REACT_100559 Reactome:REACT_101280 Reactome:REACT_101497 Reactome:REACT_102679 Reactome:REACT_103614 Reactome:REACT_104547 Reactome:REACT_105292 Reactome:REACT_105467 Reactome:REACT_105835 Reactome:REACT_106018 Reactome:REACT_106104 Reactome:REACT_106382 Reactome:REACT_106434 Reactome:REACT_106732 Reactome:REACT_107075 Reactome:REACT_107423 Reactome:REACT_108461 Reactome:REACT_108634 Reactome:REACT_108739 Reactome:REACT_108768 Reactome:REACT_108929 Reactome:REACT_109137 Reactome:REACT_112472 Reactome:REACT_113703 Reactome:REACT_29423 Reactome:REACT_29444 Reactome:REACT_29691 Reactome:REACT_29764 Reactome:REACT_30149 Reactome:REACT_31024 Reactome:REACT_31919 Reactome:REACT_32546 Reactome:REACT_32932 Reactome:REACT_33572 Reactome:REACT_33874 Reactome:REACT_50018 Reactome:REACT_53588 Reactome:REACT_6729 Reactome:REACT_6738 Reactome:REACT_6750 Reactome:REACT_6769 Reactome:REACT_6798 Reactome:REACT_6869 Reactome:REACT_6936 Reactome:REACT_6939 Reactome:REACT_77532 Reactome:REACT_79188 Reactome:REACT_79450 Reactome:REACT_80432 Reactome:REACT_80571 Reactome:REACT_80896 Reactome:REACT_80988 Reactome:REACT_81803 Reactome:REACT_83095 Reactome:REACT_84829 Reactome:REACT_85561 Reactome:REACT_86410 Reactome:REACT_86739 Reactome:REACT_87233 Reactome:REACT_87449 Reactome:REACT_87590 Reactome:REACT_88085 Reactome:REACT_88384 Reactome:REACT_88529 Reactome:REACT_89355 Reactome:REACT_89439 Reactome:REACT_89725 Reactome:REACT_90512 Reactome:REACT_90809 Reactome:REACT_90838 Reactome:REACT_91184 Reactome:REACT_91302 Reactome:REACT_92527 Reactome:REACT_92644 Reactome:REACT_92706 Reactome:REACT_94983 Reactome:REACT_95253 Reactome:REACT_95329 Reactome:REACT_96115 Reactome:REACT_96804 Reactome:REACT_96998 Reactome:REACT_97204 Reactome:REACT_97726 Reactome:REACT_99948 See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. Wikipedia:DNA_replication biological_process Loading of claspin onto DNA during replication origin firing, Xenopus tropicalis Reactome:REACT_99948 Binding of ATR-ATRIP to the RPA-ssDNA complex, Canis familiaris Reactome:REACT_87233 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Rattus norvegicus Reactome:REACT_50018 Recruitment of Rad17-RFC complex to DNA, Danio rerio Reactome:REACT_83095 Recruitment and activation of Chk1, Homo sapiens Reactome:REACT_6869 Loading of claspin onto DNA during replication origin firing, Homo sapiens Reactome:REACT_6738 Recruitment and activation of Chk1, Danio rerio Reactome:REACT_91184 Recruitment of Rad17-RFC complex to DNA, Gallus gallus Reactome:REACT_106018 Binding of ATR-ATRIP to the RPA-ssDNA complex, Rattus norvegicus Reactome:REACT_85561 Activation of claspin, Gallus gallus Reactome:REACT_88529 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Taeniopygia guttata Reactome:REACT_29764 Binding of ATR-ATRIP to the RPA-ssDNA complex, Danio rerio Reactome:REACT_84829 Activation of ATR in response to replication stress, Caenorhabditis elegans Reactome:REACT_97726 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Mus musculus Reactome:REACT_92527 Recruitment of Rad17-RFC complex to DNA, Canis familiaris Reactome:REACT_81803 Binding of ATR-ATRIP to the RPA-ssDNA complex, Gallus gallus Reactome:REACT_88085 Activation of ATR in response to replication stress, Drosophila melanogaster Reactome:REACT_108929 Activation of claspin, Xenopus tropicalis Reactome:REACT_101280 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Gallus gallus Reactome:REACT_113703 Stalling of DNA replication fork and RPA binding, Bos taurus Reactome:REACT_90512 Recruitment and activation of Chk1, Bos taurus Reactome:REACT_108461 Stalling of DNA replication fork and RPA binding, Xenopus tropicalis Reactome:REACT_94983 Activation of ATR in response to replication stress, Bos taurus Reactome:REACT_108768 Loading of claspin onto DNA during replication origin firing, Mus musculus Reactome:REACT_108634 Binding of ATR-ATRIP to the RPA-ssDNA complex, Taeniopygia guttata Reactome:REACT_29444 Activation of ATR in response to replication stress, Homo sapiens Reactome:REACT_6769 Activation of ATR in response to replication stress, Taeniopygia guttata Reactome:REACT_95253 Stalling of DNA replication fork and RPA binding, Gallus gallus Reactome:REACT_105835 Recruitment of Rad17-RFC complex to DNA, Rattus norvegicus Reactome:REACT_87449 Activation of claspin, Mus musculus Reactome:REACT_80571 Binding of ATR-ATRIP to the RPA-ssDNA complex, Xenopus tropicalis Reactome:REACT_108739 Stalling of DNA replication fork and RPA binding, Taeniopygia guttata Reactome:REACT_103614 Loading of claspin onto DNA during replication origin firing, Taeniopygia guttata Reactome:REACT_80432 Activation of ATR in response to replication stress, Xenopus tropicalis Reactome:REACT_105292 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Dictyostelium discoideum Reactome:REACT_33572 Recruitment of Rad17-RFC complex to DNA, Xenopus tropicalis Reactome:REACT_31024 Stalling of DNA replication fork and RPA binding, Homo sapiens Reactome:REACT_6936 Activation of ATR in response to replication stress, Schizosaccharomyces pombe Reactome:REACT_29423 Loading of claspin onto DNA during replication origin firing, Gallus gallus Reactome:REACT_97204 Recruitment and activation of Chk1, Rattus norvegicus Reactome:REACT_86739 Stalling of DNA replication fork and RPA binding, Canis familiaris Reactome:REACT_77532 Activation of claspin, Bos taurus Reactome:REACT_101497 Loading of claspin onto DNA during replication origin firing, Rattus norvegicus Reactome:REACT_31919 Recruitment and activation of Chk1, Taeniopygia guttata Reactome:REACT_32932 Recruitment of Rad17-RFC complex to DNA, Homo sapiens Reactome:REACT_6798 Activation of ATR in response to replication stress, Danio rerio Reactome:REACT_107075 Activation of ATR in response to replication stress, Rattus norvegicus Reactome:REACT_29691 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Schizosaccharomyces pombe Reactome:REACT_88384 Activation of claspin, Canis familiaris Reactome:REACT_106434 Recruitment of Rad17-RFC complex to DNA, Bos taurus Reactome:REACT_87590 Activation of claspin, Danio rerio Reactome:REACT_89355 Recruitment and activation of Chk1, Sus scrofa Reactome:REACT_80896 Binding of ATR-ATRIP to the RPA-ssDNA complex, Mus musculus Reactome:REACT_96115 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Caenorhabditis elegans Reactome:REACT_107423 Loading of claspin onto DNA during replication origin firing, Bos taurus Reactome:REACT_80988 Activation of claspin, Homo sapiens Reactome:REACT_6750 Recruitment and activation of Chk1, Canis familiaris Reactome:REACT_106732 Stalling of DNA replication fork and RPA binding, Danio rerio Reactome:REACT_92706 Recruitment and activation of Chk1, Gallus gallus Reactome:REACT_104547 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Xenopus tropicalis Reactome:REACT_92644 Activation of ATR in response to replication stress, Canis familiaris Reactome:REACT_91302 Stalling of DNA replication fork and RPA binding, Mus musculus Reactome:REACT_86410 Loading of claspin onto DNA during replication origin firing, Canis familiaris Reactome:REACT_53588 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Danio rerio Reactome:REACT_90809 Recruitment of Rad17-RFC complex to DNA, Taeniopygia guttata Reactome:REACT_90838 Recruitment and activation of Chk1, Xenopus tropicalis Reactome:REACT_33874 Activation of ATR in response to replication stress, Gallus gallus Reactome:REACT_102679 Activation of ATR in response to replication stress, Sus scrofa Reactome:REACT_89439 Stalling of DNA replication fork and RPA binding, Rattus norvegicus Reactome:REACT_109137 Recruitment and activation of Chk1, Mus musculus Reactome:REACT_96804 Activation of claspin, Rattus norvegicus Reactome:REACT_30149 Activation of ATR in response to replication stress, Saccharomyces cerevisiae Reactome:REACT_112472 Recruitment of Rad17-RFC complex to DNA, Mus musculus Reactome:REACT_32546 Loading of claspin onto DNA during replication origin firing, Danio rerio Reactome:REACT_105467 Activation of claspin, Taeniopygia guttata Reactome:REACT_95329 Activation of ATR in response to replication stress, Mus musculus Reactome:REACT_100559 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Canis familiaris Reactome:REACT_79188 Binding of ATR-ATRIP to the RPA-ssDNA complex, Homo sapiens Reactome:REACT_6939 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Bos taurus Reactome:REACT_96998 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Homo sapiens Reactome:REACT_6729 Activation of ATR in response to replication stress, Dictyostelium discoideum Reactome:REACT_79450 GOC:mah The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. Loading of claspin onto DNA during replication origin firing, Drosophila melanogaster Reactome:REACT_89725 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Drosophila melanogaster Reactome:REACT_106382 Binding of ATR-ATRIP to the RPA-ssDNA complex, Bos taurus Reactome:REACT_106104 transcription, DNA-templated DNA-dependent transcription GO:0006350 GO:0006351 GO:0061018 GO:0061022 The cellular synthesis of RNA on a template of DNA. Wikipedia:Transcription_(genetics) biological_process cellular transcription cellular transcription, DNA-dependent transcription transcription regulator activity transcription, DNA-dependent GOC:jl GOC:txnOH The cellular synthesis of RNA on a template of DNA. GOC:txnOH transcription, DNA-dependent translation GO:0006412 GO:0006416 GO:0006453 GO:0043037 Reactome:REACT_100338 Reactome:REACT_100851 Reactome:REACT_101045 Reactome:REACT_101324 Reactome:REACT_1014 Reactome:REACT_103420 Reactome:REACT_105544 Reactome:REACT_29980 Reactome:REACT_33559 Reactome:REACT_77710 Reactome:REACT_79784 Reactome:REACT_81734 Reactome:REACT_81833 Reactome:REACT_82171 Reactome:REACT_83429 Reactome:REACT_83530 Reactome:REACT_86996 Reactome:REACT_95535 Reactome:REACT_96394 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. Wikipedia:Translation_(genetics) biological_process protein anabolism protein biosynthesis protein biosynthetic process protein formation protein synthesis protein translation Translation, Mus musculus Reactome:REACT_95535 Translation, Bos taurus Reactome:REACT_29980 Translation, Rattus norvegicus Reactome:REACT_33559 Translation, Drosophila melanogaster Reactome:REACT_77710 GOC:go_curators The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. Translation, Caenorhabditis elegans Reactome:REACT_81833 Translation, Escherichia coli Reactome:REACT_96394 Translation, Plasmodium falciparum Reactome:REACT_103420 Translation, Canis familiaris Reactome:REACT_101324 GOC:curators protein biosynthetic process Translation, Xenopus tropicalis Reactome:REACT_82171 Translation, Gallus gallus Reactome:REACT_83530 Translation, Homo sapiens Reactome:REACT_1014 Translation, Arabidopsis thaliana Reactome:REACT_105544 Translation, Saccharomyces cerevisiae Reactome:REACT_100851 Translation, Oryza sativa Reactome:REACT_86996 Translation, Dictyostelium discoideum Reactome:REACT_101045 Translation, Danio rerio Reactome:REACT_79784 Translation, Sus scrofa Reactome:REACT_100338 Translation, Schizosaccharomyces pombe Reactome:REACT_81734 Translation, Taeniopygia guttata Reactome:REACT_83429 cellular aromatic compound metabolic process GO:0006725 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GOC:ai ISBN:0198506732 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. nitrogen compound metabolic process GO:0006807 Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium. biological_process nitrogen compound metabolism CHEBI:51143 GOC:go_curators GOC:jl ISBN:0198506732 The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium. cellular component movement GO:0006928 Note that in GO cellular components include whole cells (cell is_a cellular component). The directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore. biological_process cell movement cellular component motion GOC:dgh GOC:dph GOC:jl GOC:mlg The directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore. GOC:dph GOC:jl cellular component motion chemotaxis GO:0006935 The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). Wikipedia:Chemotaxis biological_process taxis in response to chemical stimulus ISBN:0198506732 The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). chromosome segregation GO:0007059 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. Wikipedia:Chromosome_segregation biological_process chromosome division chromosome transmission GOC:jl GOC:mah GOC:mtg_cell_cycle GOC:vw The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0000004 GO:0007582 GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. Wikipedia:Biological_process biological process biological_process physiological process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GOC:go_curators GOC:isa_complete metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. Wikipedia:Metabolism biological_process metabolic process resulting in cell growth metabolism metabolism resulting in cell growth GOC:go_curators ISBN:0198547684 The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. biosynthetic process GO:0009058 The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. Wikipedia:Anabolism anabolism biological_process biosynthesis formation synthesis GOC:curators ISBN:0198547684 The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. macromolecule biosynthetic process GO:0009059 GO:0043284 The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis CHEBI:33694 GOC:mah The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mtg_chebi_dec09 biopolymer biosynthetic process energy taxis GO:0009453 The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates. biological_process energytaxis taxis in response to energy source GOC:jl PMID:11029423 The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates. aerotaxis GO:0009454 The directed movement of a motile cell or organism in response to environmental oxygen. biological_process taxis in response to atmospheric oxygen GOC:jl ISBN:0192801023 The directed movement of a motile cell or organism in response to environmental oxygen. response to external stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. GO:0009605 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. biological_process response to environmental stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. GOC:hb spore germination GO:0009847 The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall). biological_process GOC:lr The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall). negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0009892 biological_process down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process inhibition of metabolic process negative regulation of metabolism Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0008151 GO:0009987 GO:0050875 biological_process cell growth and/or maintenance cell physiology cellular physiological process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete gene expression GO:0010467 Reactome:REACT_100537 Reactome:REACT_101147 Reactome:REACT_101952 Reactome:REACT_105649 Reactome:REACT_108313 Reactome:REACT_29068 Reactome:REACT_34240 Reactome:REACT_71 Reactome:REACT_78136 Reactome:REACT_78959 Reactome:REACT_79662 Reactome:REACT_85241 Reactome:REACT_85359 Reactome:REACT_86357 Reactome:REACT_89816 Reactome:REACT_91657 Reactome:REACT_91965 Reactome:REACT_93586 Reactome:REACT_93968 Reactome:REACT_94814 Reactome:REACT_98256 The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. Wikipedia:Gene_expression biological_process Gene Expression, Saccharomyces cerevisiae Reactome:REACT_98256 Gene Expression, Rattus norvegicus Reactome:REACT_91965 Gene Expression, Canis familiaris Reactome:REACT_86357 Gene Expression, Danio rerio Reactome:REACT_101147 Gene Expression, Homo sapiens Reactome:REACT_71 Gene Expression, Schizosaccharomyces pombe Reactome:REACT_94814 Gene Expression, Mycobacterium tuberculosis Reactome:REACT_89816 Gene Expression, Taeniopygia guttata Reactome:REACT_78959 Gene Expression, Plasmodium falciparum Reactome:REACT_79662 Gene Expression, Drosophila melanogaster Reactome:REACT_105649 Gene Expression, Sus scrofa Reactome:REACT_101952 Gene Expression, Escherichia coli Reactome:REACT_29068 Gene Expression, Staphylococcus aureus N315 Reactome:REACT_34240 Gene Expression, Oryza sativa Reactome:REACT_85241 Gene Expression, Caenorhabditis elegans Reactome:REACT_108313 Gene Expression, Dictyostelium discoideum Reactome:REACT_93586 Gene Expression, Bos taurus Reactome:REACT_93968 Gene Expression, Arabidopsis thaliana Reactome:REACT_91657 Gene Expression, Mus musculus Reactome:REACT_78136 Gene Expression, Gallus gallus Reactome:REACT_85359 Gene Expression, Xenopus tropicalis Reactome:REACT_100537 GOC:dph GOC:tb The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. GO:0010468 Wikipedia:Regulation_of_gene_expression biological_process regulation of gene product expression regulation of protein expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb GOC:curators regulation of gene product expression GOC:curators regulation of protein expression negative regulation of macromolecule metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0010605 biological_process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb negative regulation of gene expression Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. GO:0010629 biological_process Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb RNA metabolic process GO:0016070 RNA metabolism Reactome:REACT_107259 Reactome:REACT_107652 Reactome:REACT_110289 Reactome:REACT_21257 Reactome:REACT_30579 Reactome:REACT_31367 Reactome:REACT_33720 Reactome:REACT_80071 Reactome:REACT_83630 Reactome:REACT_84169 Reactome:REACT_85788 Reactome:REACT_88316 Reactome:REACT_89992 Reactome:REACT_91556 Reactome:REACT_92152 Reactome:REACT_94876 Reactome:REACT_99403 Reactome:REACT_99885 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. biological_process Metabolism of RNA, Schizosaccharomyces pombe Reactome:REACT_107652 Metabolism of RNA, Arabidopsis thaliana Reactome:REACT_94876 Metabolism of RNA, Drosophila melanogaster Reactome:REACT_92152 Metabolism of RNA, Caenorhabditis elegans Reactome:REACT_80071 Metabolism of RNA, Bos taurus Reactome:REACT_91556 Metabolism of RNA, Oryza sativa Reactome:REACT_85788 ISBN:0198506732 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Metabolism of RNA, Xenopus tropicalis Reactome:REACT_30579 Metabolism of RNA, Danio rerio Reactome:REACT_110289 Metabolism of RNA, Sus scrofa Reactome:REACT_107259 Metabolism of RNA, Dictyostelium discoideum Reactome:REACT_31367 Metabolism of RNA, Mus musculus Reactome:REACT_88316 Metabolism of RNA, Rattus norvegicus Reactome:REACT_99403 Metabolism of RNA, Homo sapiens Reactome:REACT_21257 Metabolism of RNA, Canis familiaris Reactome:REACT_84169 Metabolism of RNA, Plasmodium falciparum Reactome:REACT_33720 Metabolism of RNA, Gallus gallus Reactome:REACT_99885 Metabolism of RNA, Saccharomyces cerevisiae Reactome:REACT_89992 Metabolism of RNA, Taeniopygia guttata Reactome:REACT_83630 gene silencing Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. GO:0016458 Note that this process is the opposite of long-term maintenance of gene activation. Wikipedia:Gene_silencing biological_process long-term maintenance of gene inactivation Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. GOC:dph GOC:jid GOC:tb heterocycle biosynthetic process GO:0018130 The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). biological_process heterocycle anabolism heterocycle biosynthesis heterocycle formation heterocycle synthesis ISBN:0198547684 The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0019222 biological_process regulation of metabolism Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators aromatic compound biosynthetic process GO:0019438 The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound anabolism aromatic compound biosynthesis aromatic compound formation aromatic compound synthesis aromatic hydrocarbon biosynthesis aromatic hydrocarbon biosynthetic process biological_process GOC:ai The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. protein metabolic process GO:0006411 GO:0019538 The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. Wikipedia:Protein_metabolism biological_process protein metabolic process and modification protein metabolism protein metabolism and modification GOC:ma The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. asexual reproduction GO:0019954 The biological process in which new individuals are produced by either a single cell or a group of cells, in the absence of any sexual process. Wikipedia:Asexual_reproduction biological_process ISBN:0387520546 The biological process in which new individuals are produced by either a single cell or a group of cells, in the absence of any sexual process. cell cycle process GO:0022402 The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GOC:isa_complete GOC:mtg_cell_cycle The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. cell differentiation GO:0030154 The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. Wikipedia:Cellular_differentiation biological_process ISBN:0198506732 The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. sporulation resulting in formation of a cellular spore GO:0030435 Note that the synonym 'spore differentiation', like the term name and definition, refers to differentiation into a spore rather than any subsequent developmental changes that a spore may undergo. The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction. Wikipedia:Sporogenesis biological_process cellular spore formation by sporulation spore biosynthesis spore differentiation spore formation GOC:mah GOC:pamgo_curators ISBN:0072992913 The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction. GOC:dph GOC:tb cellular spore formation by sporulation asexual sporulation GO:0030436 The formation of spores derived from the products of mitosis. Examples of this process are found in Bacterial species. asexual spore formation biological_process mitotic spore formation mitotic sporulation GOC:mah PMID:9529886 The formation of spores derived from the products of mitosis. Examples of this process are found in Bacterial species. envelope A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GO:0031975 cellular_component A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GOC:mah GOC:pz transposition Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. GO:0032196 Wikipedia:Transposon biological_process Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. GOC:jp ISBN:1555812090 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GO:0032502 biological_process development A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete RNA biosynthetic process GO:0032774 RNA anabolism RNA biosynthesis RNA formation RNA synthesis The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. biological_process GOC:mah The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. endospore formation GO:0034301 The process in which a cell gives rise to an endospore, a dormant, highly resistant spore with a thick wall that forms within the mother cell. Endospores are produced by some low G+C Gram-positive bacteria in response to harsh conditions. biological_process GOC:ds GOC:mah ISBN:0470090278 The process in which a cell gives rise to an endospore, a dormant, highly resistant spore with a thick wall that forms within the mother cell. Endospores are produced by some low G+C Gram-positive bacteria in response to harsh conditions. myxospore formation GO:0034303 The process in which differentiated, resting cells are formed, usually within a fruiting body by Myxobacteria. The myxospore is more resistant to high temperature, dessication, and UV than vegetative myxobacteria. biological_process GOC:ds ISBN:0122268008 The process in which differentiated, resting cells are formed, usually within a fruiting body by Myxobacteria. The myxospore is more resistant to high temperature, dessication, and UV than vegetative myxobacteria. cellular nitrogen compound metabolic process GO:0034641 Reactome:REACT_102000 Reactome:REACT_103710 Reactome:REACT_107293 Reactome:REACT_108179 Reactome:REACT_109042 Reactome:REACT_13 Reactome:REACT_28699 Reactome:REACT_29108 Reactome:REACT_32429 Reactome:REACT_33347 Reactome:REACT_34326 Reactome:REACT_55564 Reactome:REACT_77741 Reactome:REACT_82379 Reactome:REACT_86268 Reactome:REACT_90299 Reactome:REACT_91959 Reactome:REACT_93580 Reactome:REACT_95666 Reactome:REACT_98086 Reactome:REACT_99241 The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. biological_process cellular nitrogen compound metabolism Metabolism of amino acids and derivatives, Dictyostelium discoideum Reactome:REACT_98086 Metabolism of amino acids and derivatives, Caenorhabditis elegans Reactome:REACT_29108 Metabolism of amino acids and derivatives, Rattus norvegicus Reactome:REACT_32429 GOC:mah The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. Metabolism of amino acids and derivatives, Saccharomyces cerevisiae Reactome:REACT_28699 Metabolism of amino acids and derivatives, Xenopus tropicalis Reactome:REACT_108179 Metabolism of amino acids and derivatives, Sus scrofa Reactome:REACT_109042 Metabolism of amino acids and derivatives, Canis familiaris Reactome:REACT_95666 Metabolism of amino acids and derivatives, Taeniopygia guttata Reactome:REACT_77741 Metabolism of amino acids and derivatives, Mus musculus Reactome:REACT_33347 Metabolism of amino acids and derivatives, Oryza sativa Reactome:REACT_90299 Metabolism of amino acids and derivatives, Homo sapiens Reactome:REACT_13 Metabolism of amino acids and derivatives, Escherichia coli Reactome:REACT_103710 Metabolism of amino acids and derivatives, Gallus gallus Reactome:REACT_55564 Metabolism of amino acids and derivatives, Arabidopsis thaliana Reactome:REACT_107293 Metabolism of amino acids and derivatives, Mycobacterium tuberculosis Reactome:REACT_102000 Metabolism of amino acids and derivatives, Staphylococcus aureus N315 Reactome:REACT_34326 Metabolism of amino acids and derivatives, Plasmodium falciparum Reactome:REACT_91959 Metabolism of amino acids and derivatives, Drosophila melanogaster Reactome:REACT_86268 Metabolism of amino acids and derivatives, Danio rerio Reactome:REACT_93580 Metabolism of amino acids and derivatives, Schizosaccharomyces pombe Reactome:REACT_99241 Metabolism of amino acids and derivatives, Bos taurus Reactome:REACT_82379 cellular macromolecule biosynthetic process GO:0034645 GO:0034961 The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. biological_process cellular biopolymer biosynthetic process cellular macromolecule anabolism cellular macromolecule biosynthesis cellular macromolecule formation cellular macromolecule synthesis GOC:mtg_chebi_dec09 cellular biopolymer biosynthetic process GOC:mah cellular macromolecule anabolism GOC:mah cellular macromolecule formation GOC:mah cellular macromolecule biosynthesis GOC:mah cellular macromolecule synthesis CHEBI:33694 GOC:mah The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. nucleobase-containing compound biosynthetic process GO:0034654 The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. biological_process nucleobase, nucleoside, nucleotide and nucleic acid anabolism nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis nucleobase, nucleoside, nucleotide and nucleic acid formation nucleobase, nucleoside, nucleotide and nucleic acid synthesis GOC:mah The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. growth GO:0040007 GO:0048590 See also the biological process term 'cell growth ; GO:0016049'. The increase in size or mass of an entire organism, a part of an organism or a cell. biological_process growth pattern non-developmental growth GOC:mah non-developmental growth GOC:bf GOC:ma The increase in size or mass of an entire organism, a part of an organism or a cell. locomotion GO:0040011 Self-propelled movement of a cell or organism from one location to another. biological_process GOC:dgh Self-propelled movement of a cell or organism from one location to another. response to chemical Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GO:0042221 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. biological_process response to chemical stimulus response to chemical substance GOC:dos response to chemical stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:jl taxis GO:0042330 The directed movement of a motile cell or organism in response to an external stimulus. Wikipedia:Taxis biological_process directed movement in response to stimulus GOC:jl ISBN:0192801023 The directed movement of a motile cell or organism in response to an external stimulus. cell projection A prolongation or process extending from a cell, e.g. a flagellum or axon. GO:0042995 cell process cellular process cellular projection cellular_component A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl http://www.cogsci.princeton.edu/~wn/ type IV pilus-dependent motility Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility. GO:0043107 TFP-dependent motility TFP-dependent movement biological_process social gliding motility twitching motility type 4 pilus-dependent motility type four pilus-dependent motility Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility. GOC:go_curators PMID:12704238 heterocyst differentiation GO:0043158 The process in which a relatively unspecialized cell acquires specialized features of a heterocyst, a differentiated cell in certain cyanobacteria whose purpose is to fix nitrogen. biological_process heterocyst biosynthesis heterocyst cell differentiation heterocyst formation GOC:jl The process in which a relatively unspecialized cell acquires specialized features of a heterocyst, a differentiated cell in certain cyanobacteria whose purpose is to fix nitrogen. macromolecule metabolic process GO:0043170 GO:0043283 The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process biopolymer metabolic process macromolecule metabolism GOC:mtg_chebi_dec09 biopolymer metabolic process CHEBI:33694 GOC:mah The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. sporulation GO:0043934 The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction. Wikipedia:Spore biological_process GOC:pamgo_curators The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction. asexual sporulation resulting in formation of a cellular spore GO:0043936 The formation of a cellular spore derived from the products of mitosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction. biological_process GOC:pamgo_curators The formation of a cellular spore derived from the products of mitosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction. cellular metabolic process GO:0044237 The chemical reactions and pathways by which individual cells transform chemical substances. biological_process cellular metabolism intermediary metabolism GOC:mah intermediary metabolism GOC:go_curators The chemical reactions and pathways by which individual cells transform chemical substances. primary metabolic process GO:0044238 The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. biological_process primary metabolism GOC:go_curators The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. http://www.metacyc.org cellular biosynthetic process GO:0044249 The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. biological_process cellular anabolism cellular biosynthesis cellular formation cellular synthesis GOC:jl The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular macromolecule metabolic process GO:0034960 GO:0044260 The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. biological_process cellular biopolymer metabolic process cellular macromolecule metabolism CHEBI:33694 GOC:mah The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. GOC:mtg_chebi_dec09 cellular biopolymer metabolic process cellular protein metabolic process GO:0044267 Reactome:REACT_101554 Reactome:REACT_102155 Reactome:REACT_105825 Reactome:REACT_106151 Reactome:REACT_108005 Reactome:REACT_109022 Reactome:REACT_17015 Reactome:REACT_32904 Reactome:REACT_34473 Reactome:REACT_80561 Reactome:REACT_81994 Reactome:REACT_82523 Reactome:REACT_85873 Reactome:REACT_86658 Reactome:REACT_89852 Reactome:REACT_91052 Reactome:REACT_93132 Reactome:REACT_96466 Reactome:REACT_99179 The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. biological_process cellular protein metabolism Metabolism of proteins, Bos taurus Reactome:REACT_108005 Metabolism of proteins, Danio rerio Reactome:REACT_82523 Metabolism of proteins, Saccharomyces cerevisiae Reactome:REACT_85873 Metabolism of proteins, Oryza sativa Reactome:REACT_99179 Metabolism of proteins, Taeniopygia guttata Reactome:REACT_34473 Metabolism of proteins, Xenopus tropicalis Reactome:REACT_106151 Metabolism of proteins, Escherichia coli Reactome:REACT_80561 Metabolism of proteins, Dictyostelium discoideum Reactome:REACT_105825 Metabolism of proteins, Arabidopsis thaliana Reactome:REACT_102155 Metabolism of proteins, Sus scrofa Reactome:REACT_81994 Metabolism of proteins, Homo sapiens Reactome:REACT_17015 Metabolism of proteins, Schizosaccharomyces pombe Reactome:REACT_109022 Metabolism of proteins, Gallus gallus Reactome:REACT_101554 Metabolism of proteins, Canis familiaris Reactome:REACT_32904 Metabolism of proteins, Mus musculus Reactome:REACT_93132 Metabolism of proteins, Plasmodium falciparum Reactome:REACT_96466 GOC:jl The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. Metabolism of proteins, Rattus norvegicus Reactome:REACT_89852 Metabolism of proteins, Drosophila melanogaster Reactome:REACT_86658 Metabolism of proteins, Caenorhabditis elegans Reactome:REACT_91052 cellular nitrogen compound biosynthetic process GO:0044271 The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. biological_process nitrogen compound anabolism nitrogen compound biosynthesis nitrogen compound formation nitrogen compound synthesis GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. cell part Any constituent part of a cell, the basic structural and functional unit of all organisms. GO:0044464 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular subcomponent cellular_component protoplast NIF_Subcellular:sao628508602 cellular subcomponent Any constituent part of a cell, the basic structural and functional unit of all organisms. GOC:jl GOC:mah protoplast single-organism process A biological process that involves only one organism. GO:0044699 biological_process single organism process A biological process that involves only one organism. GOC:jl single-organism metabolic process A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism. GO:0044710 biological_process A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism. GOC:jl single-organism biosynthetic process A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - involving a single organism. GO:0044711 biological_process A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - involving a single organism. GOC:jl single-organism cellular process Any process that is carried out at the cellular level, occurring within a single organism. GO:0044763 biological_process Any process that is carried out at the cellular level, occurring within a single organism. GOC:jl single-organism developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism. GO:0044767 biological_process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism. GOC:jl cell cycle DNA replication GO:0044786 The DNA-dependent DNA replication that takes place as part of the cell cycle. biological_process GOC:mtg_cell_cycle The DNA-dependent DNA replication that takes place as part of the cell cycle. heterocycle metabolic process GO:0046483 The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). biological_process heterocycle metabolism CHEBI:5686 ISBN:0198506732 The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). negative regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043118 GO:0048519 biological_process down regulation of biological process down-regulation of biological process downregulation of biological process inhibition of biological process negative regulation of physiological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid anatomical structure formation involved in morphogenesis GO:0048646 Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. biological_process formation of an anatomical structure involved in morphogenesis GOC:dph GOC:jid GOC:tb The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GOC:dph GOC:tb formation of an anatomical structure involved in morphogenesis cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GO:0048869 biological_process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GOC:isa_complete cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GO:0048870 biological_process cell locomotion cell movement movement of a cell Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GOC:dgh GOC:dph GOC:isa_complete GOC:mlg regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050789 GO:0050791 biological_process regulation of physiological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0050896 GO:0051869 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. biological_process physiological response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location. GO:0051179 biological_process establishment and maintenance of cellular component location establishment and maintenance of localization establishment and maintenance of position establishment and maintenance of substance location establishment and maintenance of substrate location localisation Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location. GOC:ai GOC:mah localisation regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0060255 biological_process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GO:0065007 biological_process regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw organic substance metabolic process GO:0071704 The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. biological_process organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism CHEBI:50860 GOC:mah The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. bacterial-type flagellum-dependent cell motility Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope. GO:0071973 bacterial-type flagellar cell motility biological_process flagellin-based flagellar cell motility GOC:mah flagellin-based flagellar cell motility Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope. GOC:cilia GOC:krc GOC:mah cell swimming Cell motility that results in the smooth movement of a cell through a liquid medium. GO:0071975 biological_process cell swimming motility Cell motility that results in the smooth movement of a cell through a liquid medium. PMID:18461074 GOC:mah cell swimming motility cell gliding Cell motility that results in the smooth movement of a cell along a solid surface. GO:0071976 biological_process cell gliding motility Cell motility that results in the smooth movement of a cell along a solid surface. PMID:18461074 GOC:mah cell gliding motility bacterial-type flagellum-dependent swarming motility Bacterial-type flagellum-dependent cell motility in which the action of numerous flagella results in the smooth movement of a group of cells along a solid surface. Swarming motility is observed in groups of bacteria. GO:0071978 bacterial-type flagellar swarming motility bacterial-type flagellum-mediated cell swarming biological_process GOC:mah bacterial-type flagellum-mediated cell swarming Bacterial-type flagellum-dependent cell motility in which the action of numerous flagella results in the smooth movement of a group of cells along a solid surface. Swarming motility is observed in groups of bacteria. GOC:cilia PMID:14527279 PMID:18461074 nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. GO:0090304 biological_process Any cellular metabolic process involving nucleic acids. GOC:dph GOC:tb archaeal or bacterial-type flagellum-dependent cell motility Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. This term was added for mapping to the UniProt keyword "flagellar rotation". For manual annotation, please use one of the child terms of GO:0097588 that refer specifically to either archaeal- or bacterial-type flagella. Cell motility due to movement of bacterial- or archaeal-type flagella. GO:0097588 biological_process Cell motility due to movement of bacterial- or archaeal-type flagella. GOC:cilia GOC:krc organic cyclic compound metabolic process GO:1901360 The chemical reactions and pathways involving organic cyclic compound. biological_process organic cyclic compound metabolism GOC:TermGenie organic cyclic compound metabolism GOC:TermGenie The chemical reactions and pathways involving organic cyclic compound. organic cyclic compound biosynthetic process GO:1901362 The chemical reactions and pathways resulting in the formation of organic cyclic compound. biological_process organic cyclic compound anabolism organic cyclic compound biosynthesis organic cyclic compound formation organic cyclic compound synthesis GOC:TermGenie organic cyclic compound anabolism GOC:TermGenie organic cyclic compound formation GOC:TermGenie organic cyclic compound synthesis GOC:TermGenie The chemical reactions and pathways resulting in the formation of organic cyclic compound. GOC:TermGenie organic cyclic compound biosynthesis organic substance biosynthetic process GO:1901576 The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. biological_process organic molecular entity anabolism organic molecular entity biosynthesis organic molecular entity biosynthetic process organic molecular entity formation organic molecular entity synthesis organic substance anabolism organic substance biosynthesis organic substance formation organic substance synthesis GOC:TermGenie organic molecular entity biosynthesis GOC:TermGenie organic molecular entity anabolism GOC:TermGenie GOC:pr The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. GOC:TermGenie organic molecular entity synthesis GOC:TermGenie organic molecular entity formation microbial phenotype 2011-03-10T04:01:50Z OMP:0000000 The observable manifestation of the genotype of a microbial cell or group of cells in an environment. microbial_phenotype OMP:MCC The observable manifestation of the genotype of a microbial cell or group of cells in an environment. motility phenotype 2011-03-10T06:55:06Z A locomotion phenotype where the trait in question is the self-propelled movement of a microbe from one location to another. GO:0048870 OMP:0000001 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A locomotion phenotype where the trait in question is the self-propelled movement of a microbe from one location to another. OMP:MCC cell motility GO:0048870 decreased motility 2011-03-10T07:02:42Z An altered motility phenotype where the frequency, rate, timing, or extent of a microbe's motility is decreased relative to a designated control. OMP:0000002 PATO:0002297 microbial_phenotype An altered motility phenotype where the frequency, rate, timing, or extent of a microbe's motility is decreased relative to a designated control. OMP:MCC cell arrangement phenotype 2011-04-14T02:30:07Z A microbial phenotype where the trait in question is the arrangement of cells of a microbe in relation to one another. OMP:0000003 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A microbial phenotype where the trait in question is the arrangement of cells of a microbe in relation to one another. OMP:MCC taxis phenotype 2011-04-14T03:29:20Z A locomotion phenotype where the directed movement of a motile microbe is in response to an external stimulus. OMP:0000004 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A locomotion phenotype where the directed movement of a motile microbe is in response to an external stimulus. ISBN:0192800329 OMP:MCC presence of motility 2011-04-14T03:35:35Z A motility phenotype where a microbe possesses the ability to perform controlled self-propelled movement that results in translocation from one place to another. OMP:0000005 mchibucos microbial_phenotype motile A motility phenotype where a microbe possesses the ability to perform controlled self-propelled movement that results in translocation from one place to another. OMP:MCC presence of akinete formation 2011-04-26T02:51:36Z An akinete formation phenotype where a cell or cells have the ability to differentiate into an akinete. OMP:0000006 mchibucos microbial_phenotype An akinete formation phenotype where a cell or cells have the ability to differentiate into an akinete. OMP:MCC absence of akinete formation 2011-04-26T02:52:52Z An akinete formation phenotype where a cell or cells do not possess the ability to form an akinete. OMP:0000007 mchibucos microbial_phenotype An akinete formation phenotype where a cell or cells do not possess the ability to form an akinete. OMP:MCC presence of budding 2011-04-26T02:58:46Z A budding phenotype where an organism reproduces by the process of budding. OMP:0000008 mchibucos microbial_phenotype A budding phenotype where an organism reproduces by the process of budding. OMP:MCC decreased cell surface area-to-volume ratio 2020-07-22T22:22:03Z OMP:0000009 microbial_phenotype siegele presence of heterocysts 2011-04-26T02:59:42Z A heterocyst formation phenotype where a cell possesses the ability to differentiate into a heterocyst. OMP:0000010 mchibucos microbial_phenotype A heterocyst formation phenotype where a cell possesses the ability to differentiate into a heterocyst. OMP:MCC absence of heterocysts 2011-04-26T02:59:42Z A heterocyst formation phenotype where an organism does not possess the ability to differentiate into a heterocyst. OMP:0000011 mchibucos microbial_phenotype A heterocyst formation phenotype where an organism does not possess the ability to differentiate into a heterocyst. OMP:MCC abolished spore germination efficiency 2011-04-26T03:01:38Z A decreased spore germination phenotype where no spores germinate. OMP:0000012 mchibucos microbial_phenotype A decreased spore germination phenotype where no spores germinate. OMP:MCC decreased endospore formation 2011-06-07T10:14:15Z An altered endospore formation phenotype where the rate, frequency, timing, or extent of endospore formation is decreased relative to a designated control. OMP:0000013 mchibucos microbial_phenotype An altered endospore formation phenotype where the rate, frequency, timing, or extent of endospore formation is decreased relative to a designated control. OMP:JCH increased endospore formation 2011-06-07T10:14:39Z An altered endospore formation phenotype where the rate, frequency, timing, or extent of endospore formation is increased relative to a designated control. OMP:0000014 mchibucos microbial_phenotype An altered endospore formation phenotype where the rate, frequency, timing, or extent of endospore formation is increased relative to a designated control. OMP:JCH decreased heterocyst formation 2011-04-26T03:05:35Z A heterocyst formation phenotype where heterocyst formation is decreased relative to a designated control. OMP:0000015 mchibucos microbial_phenotype A heterocyst formation phenotype where heterocyst formation is decreased relative to a designated control. OMP:MCC delayed spore germination 2011-04-26T03:07:11Z A spore germination phenotype where a spore undergoes germination after a longer than usual dormancy period. OMP:0000016 mchibucos microbial_phenotype A spore germination phenotype where a spore undergoes germination after a longer than usual dormancy period. OMP:MCC presence of endospore formation 2011-04-26T03:09:10Z An endospore formation phenotype where the cell possesses the ability to form an endospore. OMP:0000017 mchibucos microbial_phenotype An endospore formation phenotype where the cell possesses the ability to form an endospore. OMP:MCC absence of endospore formation 2011-04-26T03:09:25Z An endospore formation phenotype where the cell does not possess the ability to form an endospore. OMP:0000018 mchibucos microbial_phenotype An endospore formation phenotype where the cell does not possess the ability to form an endospore. OMP:MCC increased cell surface area-to-volume ratio 2020-07-22T22:22:03Z OMP:0000019 microbial_phenotype siegele presence of myxospore formation 2011-04-26T03:10:51Z A myxospore formation phenotype where an organism possesses the ability to form myxospores. OMP:0000020 mchibucos microbial_phenotype A myxospore formation phenotype where an organism possesses the ability to form myxospores. OMP:MCC absence of myxospore formation 2011-04-26T03:10:51Z A myxospore formation phenotype where an organism does not possess the ability to form myxospores. OMP:0000021 mchibucos microbial_phenotype A myxospore formation phenotype where an organism does not possess the ability to form myxospores. OMP:MCC decreased myxospore formation 2011-04-26T03:10:51Z An altered myxospore formation phenotype where the rate, frequency, timing, or extent of myxospore formation is decreased relative to a designated control. OMP:0000022 mchibucos microbial_phenotype An altered myxospore formation phenotype where the rate, frequency, timing, or extent of myxospore formation is decreased relative to a designated control. OMP:MCC periplasmic flagellum/flagella 2011-06-07T11:12:48Z A flagellum distribution phenotype where the flagellum filament of an organism is located in the periplasm and does not extend past the cell envelope. OMP:0000023 axial fibril axial filament endoflagella mchibucos microbial_phenotype A flagellum distribution phenotype where the flagellum filament of an organism is located in the periplasm and does not extend past the cell envelope. ISBN:9780073402406 OMP:DAS altered flagellum length 2011-06-07T11:19:56Z An altered flagellum phenotype where the length of the flagellum is altered relative to a designated control. OMP:0000024 mchibucos microbial_phenotype An altered flagellum phenotype where the length of the flagellum is altered relative to a designated control. OMP:MCC altered cell surface area-to-volume ratio variability 2020-07-22T22:23:15Z OMP:0000025 microbial_phenotype siegele host-virus interaction phenotype 2011-06-06T02:39:55Z A microbial phenotype related to the ability of a host to be infected by and/or support reproduction of a virus. OMP:0000026 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. host-bacteriophage interaction phenotype host-phage interaction phenotype mchibucos microbial_phenotype A microbial phenotype related to the ability of a host to be infected by and/or support reproduction of a virus. OMP:JCH flagellum morphology phenotype 2011-04-26T03:26:26Z A cell projection morphology phenotype relating to the size, shape, or appearance of flagella, which are threadlike structures borne either singly or in groups by a motile cell, which propel the cell. OMP:0000027 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. axial filament phenotype mchibucos microbial_phenotype A cell projection morphology phenotype relating to the size, shape, or appearance of flagella, which are threadlike structures borne either singly or in groups by a motile cell, which propel the cell. OMP:MCC decreased number of pili 2011-04-26T03:29:28Z A presence of pilus phenotype where a microorganism has fewer pili per cell relative to a designated control. OMP:0000028 decreased fimbriae formation mchibucos microbial_phenotype A presence of pilus phenotype where a microorganism has fewer pili per cell relative to a designated control. OMP:MCC presence of flagellum 2011-04-26T03:29:34Z A flagellum phenotype where the organism possesses a flagellum or flagella in at least some environments. OMP:0000029 mchibucos microbial_phenotype A flagellum phenotype where the organism possesses a flagellum or flagella in at least some environments. OMP:MCC absence of flagellum 2011-04-26T03:29:50Z A flagellum phenotype where the organism does not possess a flagellum or flagella. OMP:0000030 mchibucos microbial_phenotype non-flagellated phenotype A flagellum phenotype where the organism does not possess a flagellum or flagella. OMP:MCC altered flagellum shape 2011-04-26T03:41:37Z An altered flagellum phenotype where the shape of the flagellum is altered relative to a designated control. OMP:0000031 mchibucos microbial_phenotype An altered flagellum phenotype where the shape of the flagellum is altered relative to a designated control. OMP:MCC decreased cell surface area-to-volume ratio variability 2020-07-22T22:24:44Z OMP:0000032 microbial_phenotype siegele absence of pilus 2011-04-26T03:44:01Z A pilus phenotype where an organism does not possess a pilus. OMP:0000033 fimbria absent mchibucos microbial_phenotype A pilus phenotype where an organism does not possess a pilus. OMP:MCC presence of pilus 2011-04-26T03:44:22Z A pilus phenotype where a microorganism produces a pilus or pili in one or more growth conditions. Fimbria (plural, fimbriae) is a common synonym for pilus (plural, pili). OMP:0000034 fimbria present mchibucos microbial_phenotype A pilus phenotype where a microorganism produces a pilus or pili in one or more growth conditions. OMP:MCC malformed pilus 2011-04-26T03:44:34Z A pilus phenotype where the cell possesses a pilus that was distorted during formation. OMP:0000035 malformed fimbrium mchibucos microbial_phenotype A pilus phenotype where the cell possesses a pilus that was distorted during formation. OMP:MCC increased amount of capsule 2011-06-07T10:53:11Z An altered capsule phenotype where the amount of capsule is increased relative to a designated control. OMP:0000036 mchibucos microbial_phenotype An altered capsule phenotype where the amount of capsule is increased relative to a designated control. OMP:DAS increased flagellum length 2011-06-07T11:25:05Z An altered flagellum length phenotype where the length of the flagellum is longer than a designated control. OMP:0000037 mchibucos microbial_phenotype An altered flagellum length phenotype where the length of the flagellum is longer than a designated control. OMP:MCC increased cell surface area-to-volume ratio variability 2020-07-22T22:24:44Z OMP:0000038 microbial_phenotype siegele O2 effects on population growth phenotype 2011-06-06T03:36:04Z A population growth range phenotype related to how growth of a microbial population is affected by different concentrations of oxygen gas (O2) in the environment. OMP:0000039 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A population growth range phenotype related to how growth of a microbial population is affected by different concentrations of oxygen gas (O2) in the environment. OMP:WAM decreased cell size 2011-04-26T03:47:26Z An altered cell size phenotype where the size of a cell or cells is decreased relative to a designated control. OMP:0000040 mchibucos microbial_phenotype An altered cell size phenotype where the size of a cell or cells is decreased relative to a designated control. OMP:MCC increased cell size 2011-04-26T03:49:09Z An altered cell size phenotype where the volume of a cell or cells is increased relative to a designated control. OMP:0000041 mchibucos microbial_phenotype An altered cell size phenotype where the volume of a cell or cells is increased relative to a designated control. OMP:MCC anucleoid 2011-04-26T03:51:47Z A nucleoid phenotype where the nucleoid is absent in some fraction of cells in a population. OMP:0000042 mchibucos microbial_phenotype A nucleoid phenotype where the nucleoid is absent in some fraction of cells in a population. OMP:DAS nucleoid number phenotype 2011-04-26T03:53:34Z A nucleoid phenotype dealing with the number of nucleoid regions in the cell. OMP:0000043 mchibucos microbial_phenotype A nucleoid phenotype dealing with the number of nucleoid regions in the cell. OMP:WAM altered cell circularity 2020-07-22T22:30:41Z Cell circularity is defined as (2*pi*cell area/(cell perimeter)^2). OMP:0000044 microbial_phenotype siegele Cell circularity is defined as (2*pi*cell area/(cell perimeter)^2). OMP:das increased motility 2011-04-26T04:08:26Z An altered motility phenotype where the frequency, rate, timing, or extent of motility of a microbe is increased relative to a designated control. OMP:0000045 PATO:0002298 mchibucos microbial_phenotype An altered motility phenotype where the frequency, rate, timing, or extent of motility of a microbe is increased relative to a designated control. OMP:MCC presence of chemotaxis 2011-04-26T04:17:42Z A chemotaxis phenotype where a motile microbe displays directed movement in response to a specific chemical concentration gradient. OMP:0000046 mchibucos microbial_phenotype A chemotaxis phenotype where a motile microbe displays directed movement in response to a specific chemical concentration gradient. OMP:MCC aerotaxis phenotype 2011-04-26T04:18:11Z A taxis phenotype where directed movement of a motile microbe is in response to environmental oxygen (O2). GO:0009454 OMP:0000047 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A taxis phenotype where directed movement of a motile microbe is in response to environmental oxygen (O2). ISBN:0192800329 OMP:MCC aerotaxis GO:0009454 chemotaxis phenotype 2011-04-26T04:27:11Z A taxis phenotype where the directed movement of a motile microbe is in response to a specific chemical concentration gradient. GO:0006935 OMP:0000048 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. ChEBI cross product candidate (and child terms). mchibucos microbial_phenotype A taxis phenotype where the directed movement of a motile microbe is in response to a specific chemical concentration gradient. ISBN:0198506732 OMP:MCC presence of aerotaxis 2011-04-26T04:27:42Z An aerotaxis phenotype where a motile microbe displays directed movement in response to environmental oxygen (O2). OMP:0000049 mchibucos microbial_phenotype An aerotaxis phenotype where a motile microbe displays directed movement in response to environmental oxygen (O2). OMP:MCC decreased amount of capsule 2011-06-07T10:53:59Z An altered capsule phenotype where the amount of capsule produced is decreased relative to a designated control. OMP:0000050 mchibucos microbial_phenotype An altered capsule phenotype where the amount of capsule produced is decreased relative to a designated control. OMP:DAS decreased cell circularity 2020-07-22T22:32:02Z OMP:0000051 microbial_phenotype siegele presence of positive chemotaxis 2011-04-26T04:42:14Z A presence of chemotaxis phenotype where a motile microbe displays directed movement towards a higher concentration of a chemical. OMP:0000052 mchibucos microbial_phenotype A presence of chemotaxis phenotype where a motile microbe displays directed movement towards a higher concentration of a chemical. OMP:MCC presence of negative chemotaxis 2011-04-26T04:42:14Z A presence of chemotaxis phenotype where a motile microbe displays directed movement toward a lower concentration of a chemical (away from a higher concentration of a chemical). OMP:0000053 mchibucos microbial_phenotype repellent A presence of chemotaxis phenotype where a motile microbe displays directed movement toward a lower concentration of a chemical (away from a higher concentration of a chemical). OMP:MCC absence of positive chemotaxis 2011-04-26T04:42:14Z An absence of chemotaxis phenotype where an organism doesn't display directed movement toward a higher concentration of a specific chemical. OMP:0000054 mchibucos microbial_phenotype An absence of chemotaxis phenotype where an organism doesn't display directed movement toward a higher concentration of a specific chemical. OMP:MCC absence of negative chemotaxis 2011-04-26T04:42:14Z An absence of chemotaxis phenotype where an organism doesn't display directed movement toward a lower concentration of a specific chemical. OMP:0000055 mchibucos microbial_phenotype An absence of chemotaxis phenotype where an organism doesn't display directed movement toward a lower concentration of a specific chemical. OMP:MCC presence of positive aerotaxis 2011-04-26T04:44:17Z A presence of aerotaxis phenotype where a motile cell or organism displays directed movement towards a higher concentration of environmental oxygen. GO:0052131 OMP:0000056 mchibucos microbial_phenotype A presence of aerotaxis phenotype where a motile cell or organism displays directed movement towards a higher concentration of environmental oxygen. OMP:MCC presence of negative aerotaxis 2011-04-26T04:44:17Z A presence of aerotaxis phenotype where a motile cell or organism displays directed movement towards a lower concentration of environmental oxygen. GO:0052130 OMP:0000057 mchibucos microbial_phenotype A presence of aerotaxis phenotype where a motile cell or organism displays directed movement towards a lower concentration of environmental oxygen. OMP:MCC absence of positive aerotaxis 2011-04-26T04:44:17Z An absence of aerotaxis phenotype where a motile microbe doesn't display directed movement towards a higher concentration of environmental oxygen (O2). OMP:0000058 mchibucos microbial_phenotype An absence of aerotaxis phenotype where a motile microbe doesn't display directed movement towards a higher concentration of environmental oxygen (O2). OMP:MCC absence of negative aerotaxis 2011-04-26T04:44:17Z An absence of aerotaxis phenotype where a motile microbe doesn't display directed movement away from a higher concentration of environmental oxygen (O2). OMP:0000059 mchibucos microbial_phenotype An absence of aerotaxis phenotype where a motile microbe doesn't display directed movement away from a higher concentration of environmental oxygen (O2). OMP:MCC presence of quorum sensing 2011-04-26T05:02:51Z A quorum sensing phenotype where an organism possesses the ability to monitor its population density by detecting the concentration of small, diffusible signal molecules. OMP:0000060 mchibucos microbial_phenotype A quorum sensing phenotype where an organism possesses the ability to monitor its population density by detecting the concentration of small, diffusible signal molecules. OMP:MCC decreased virulence 2011-04-26T05:02:57Z An altered virulence phenotype where the rate, frequency, timing, or extent of the ability of a microbe to cause disease in another organism (the host) is decreased relative to a designated control. OMP:0000061 PATO:0002147 less virulent mchibucos microbial_phenotype An altered virulence phenotype where the rate, frequency, timing, or extent of the ability of a microbe to cause disease in another organism (the host) is decreased relative to a designated control. OMP:MCC increased virulence 2011-04-26T05:03:12Z An altered virulence phenotype where the rate, frequency, timing, or extent of the ability of a microbe to cause disease in another organism (the host) is increased relative to a designated control. OMP:0000062 PATO:0002148 mchibucos microbial_phenotype more virulent An altered virulence phenotype where the rate, frequency, timing, or extent of the ability of a microbe to cause disease in another organism (the host) is increased relative to a designated control. OMP:MCC absence of quorum sensing 2011-04-26T05:06:00Z A quorum sensing phenotype where an organism does not possess the ability to monitor its population density by detecting the concentration of small, diffusible signal molecules. OMP:0000063 mchibucos microbial_phenotype A quorum sensing phenotype where an organism does not possess the ability to monitor its population density by detecting the concentration of small, diffusible signal molecules. OMP:MCC increased cell circularity 2020-07-22T22:32:02Z OMP:0000064 microbial_phenotype siegele absence of virulence 2011-04-26T05:06:35Z A virulence phenotype where an organism does not possess the ability to cause disease in another organism (host). OMP:0000065 avirulence incompatible interaction mchibucos microbial_phenotype A virulence phenotype where an organism does not possess the ability to cause disease in another organism (host). OMP:MCC abolished virulence 2011-04-26T05:09:24Z A decreased virulence phenotype where rate, frequency, timing, or extent of the ability of a microbe to cause disease in a host is abolished. OMP:0000066 mchibucos microbial_phenotype A decreased virulence phenotype where rate, frequency, timing, or extent of the ability of a microbe to cause disease in a host is abolished. OMP:MCC presence of motility by swarming 2011-02-02T03:28:43Z A presence of motility phenotype where a population of microbes exhibit coordinated translocation across solid or semi-solid surfaces. OMP:0000067 adrienne microbial_phenotype A presence of motility phenotype where a population of microbes exhibit coordinated translocation across solid or semi-solid surfaces. OMP:MCC virulence phenotype 2011-02-02T03:28:59Z A microbe-host interaction phenotype related to the ability of a microbe to cause disease in another organism (the host). APO:0000048 GO:0009405 OMP:0000068 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne infectious agent microbial_phenotype pathogen pathogenesis GO:0009405 virulence APO:0000048 A microbe-host interaction phenotype related to the ability of a microbe to cause disease in another organism (the host). OMP:MCC quorum sensing phenotype 2011-02-07T03:47:50Z A microbial communication phenotype where cells sense their population density by detecting the concentration of small, diffusible signal molecules produced by the cells themselves. GO:0009372 OMP:0000069 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype quorum sensing GO:0009372 A microbial communication phenotype where cells sense their population density by detecting the concentration of small, diffusible signal molecules produced by the cells themselves. GO:0009372 OMP:MCC cell development phenotype 2011-02-02T03:11:48Z A microbial phenotype where the trait in question is the progression of a cell from an initial condition to a later condition. GO:0048869 OMP:0000070 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype cellular developmental process GO:0048869 A microbial phenotype where the trait in question is the progression of a cell from an initial condition to a later condition. OMP:MCC cell morphology phenotype 2011-02-02T03:15:16Z A microbial phenotype related to the form and structure of a microbial cell. APO:0000050 OMP:0000071 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype cellular morphology APO:0000050 A microbial phenotype related to the form and structure of a microbial cell. OMP:MCC filamentous 2011-02-02T03:31:35Z A cell arrangement phenotype where cells are joined end-to-end in linear chains. OMP:0000072 adrienne microbial_phenotype A cell arrangement phenotype where cells are joined end-to-end in linear chains. OMP:MCC cell shape phenotype 2011-02-02T03:18:02Z A cell morphology phenotype where the trait in question is the shape of a cell. APO:0000051 OMP:0000073 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype cell shape APO:0000051 A cell morphology phenotype where the trait in question is the shape of a cell. OMP:MCC cell size phenotype 2011-02-02T03:18:19Z A cell morphology phenotype where the trait in question is the size of a cell. APO:0000052 OMP:0000074 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype A cell morphology phenotype where the trait in question is the size of a cell. OMP:MCC cell size APO:0000052 coccus 2011-02-02T03:18:29Z A spheroid cell phenotype where a cell is spherical or nearly spherical. OMP:0000075 adrienne microbial_phenotype spherical-shaped A spheroid cell phenotype where a cell is spherical or nearly spherical. ISBN:9780073402406 OMP:MCC rod-shaped cells 2011-02-02T03:18:47Z A cylindrical cell phenotype where an organism has rod-shaped cells. OMP:0000076 adrienne bacillus microbial_phenotype A cylindrical cell phenotype where an organism has rod-shaped cells. ISBN:9780073402406 OMP:MCC vibrio 2011-02-02T03:19:31Z A spiral cell shape phenotype where a rod-shaped cell is curved to form a comma-like shape or incomplete spiral. OMP:0000077 adrienne microbial_phenotype A spiral cell shape phenotype where a rod-shaped cell is curved to form a comma-like shape or incomplete spiral. ISBN:9780073402406 OMP:AEZ flagellum arrangement phenotype 2011-02-02T03:43:16Z A flagellum phenotype where the trait in question is the location of the flagellum on an organism. OMP:0000078 adrienne microbial_phenotype A flagellum phenotype where the trait in question is the location of the flagellum on an organism. OMP:MCC monotrichous 2011-02-02T03:44:18Z A flagellum distribution phenotype where an organism has a single flagellum. OMP:0000079 adrienne microbial_phenotype single flagellum A flagellum distribution phenotype where an organism has a single flagellum. ISBN:9780073402406 amphitrichous 2011-02-02T03:45:34Z A flagellum distribution phenotype where an organism has a single flagellum at each end of the cell. OMP:0000080 adrienne microbial_phenotype A flagellum distribution phenotype where an organism has a single flagellum at each end of the cell. ISBN:9780073402406 OMP:MCC lophotrichous 2011-02-02T03:46:16Z A flagellum distribution phenotype where an organism has multiple flagella located at one or both ends of a cell. OMP:0000081 adrienne microbial_phenotype A flagellum distribution phenotype where an organism has multiple flagella located at one or both ends of a cell. ISBN:9780073402406 peritrichous flagella 2011-02-02T03:46:44Z A flagellum distribution phenotype where an organism has multiple flagella dispersed across the cell surface. OMP:0000082 adrienne microbial_phenotype A flagellum distribution phenotype where an organism has multiple flagella dispersed across the cell surface. ISBN:9780073402406 OMP:MCC cell projection morphology phenotype 2011-02-02T03:47:44Z A cell morphology phenotype relating to the size, shape, or appearance of a structure that is a prolongation or process extending from a cell. GO:0042995 OMP:0000083 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we recommend that it not be used for direct annotation. Please consider using a more specific term to annotate each phenotype. adrienne cell appendage phenotype microbial_phenotype A cell morphology phenotype relating to the size, shape, or appearance of a structure that is a prolongation or process extending from a cell. GO:0042995 OMP:MCC cell projection GO:0042995 pilus morphology phenotype 2011-02-02T03:47:57Z A cell projection phenotype morphology where the structure in question is a proteinaceous hair-like appendage on the surface of a microbial cell. OMP:0000084 adrienne fimbria phenotype microbial_phenotype GO:0009289 fimbria phenotype A cell projection phenotype morphology where the structure in question is a proteinaceous hair-like appendage on the surface of a microbial cell. ISBN:9780073402406 OMP:MCC cell envelope morphology phenotype 2011-02-02T03:49:03Z A cell morphology phenotype relating to the size, shape, or appearance of the envelope that surrounds a microbial cell. The envelope includes the cytoplasmic membrane and everything external to the cytoplasmic membrane, encompassing the periplasmic space, cell wall, and outer membrane. Additional layers, such as capsules or S-layers, are also part of the envelope. OMP:0000085 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype A cell morphology phenotype relating to the size, shape, or appearance of the envelope that surrounds a microbial cell. The envelope includes the cytoplasmic membrane and everything external to the cytoplasmic membrane, encompassing the periplasmic space, cell wall, and outer membrane. Additional layers, such as capsules or S-layers, are also part of the envelope. OMP:MCC spiral cell shape 2011-02-02T03:19:47Z A cell shape phenotype where a cell is helical or cork-screw shaped. OMP:0000086 adrienne curved rod microbial_phenotype spirillum spirochete vibrio A cell shape phenotype where a cell is helical or cork-screw shaped. OMP:MCC facultative anaerobe 2011-06-06T03:42:26Z A microbial phenotype that describes a microorganism that does not require oxygen gas (O2) for growth but will utilize O2 in metabolic reactions when it is present. OMP:0000087 facultative aerobe mchibucos microbial_phenotype ISBN:978-0134261928 facultative aerobe A microbial phenotype that describes a microorganism that does not require oxygen gas (O2) for growth but will utilize O2 in metabolic reactions when it is present. ISBN:9780073402406 OMP:WAM filamentous colony 2011-06-07T12:08:48Z A colony form phenotype characterized by growth of thin individual projections in the colony. OMP:0000088 SNOMEDCT:31153000 mchibucos microbial_phenotype A colony form phenotype characterized by growth of thin individual projections in the colony. OMP:WAM budding phenotype 2011-02-02T03:23:41Z An asexual reproduction phenotype related to the process of budding, where a new individual forms from an outgrowth (bud) on the body of the parental organism. GO:0007114 OMP:0000089 adrienne microbial_phenotype An asexual reproduction phenotype related to the process of budding, where a new individual forms from an outgrowth (bud) on the body of the parental organism. OMP:DAS cell budding GO:0007114 lifespan phenotype 2011-02-02T03:24:11Z An organismal growth phenotype dealing with the lifespan of a microorganism, cell, or cells. OMP:0000090 adrienne microbial_phenotype An organismal growth phenotype dealing with the lifespan of a microorganism, cell, or cells. OMP:WAM sporulation phenotype 2011-02-02T03:24:24Z A cell development phenotype related to formation of a spore, a dormant differentiated cell that can be used for dissemination, survival in adverse conditions, or reproduction. GO:0043934 OMP:0000091 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype sporulation GO:0043934 A cell development phenotype related to formation of a spore, a dormant differentiated cell that can be used for dissemination, survival in adverse conditions, or reproduction. OMP:MCC heterocyst formation phenotype 2011-02-02T03:24:43Z A cell development phenotype related to development of a heterocyst, a differentiated cell in certain cyanobacteria whose purpose is to fix nitrogen. GO:0043158 OMP:0000092 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype A cell development phenotype related to development of a heterocyst, a differentiated cell in certain cyanobacteria whose purpose is to fix nitrogen. DOI:10.1046/j.1469-8137.1999.00505.x OMP:MCC heterocyst differentiation GO:0043158 akinete formation phenotype 2011-02-02T03:25:02Z A cell development phenotype related to the development of an akinete, a thick-walled dormant cell derived from the enlargement of a vegetative cell. GO:0034302 OMP:0000093 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Akinetes typically are more resistant to dessication and other environmental stresses than vegetative cells. adrienne microbial_phenotype akinete formation GO:0034302 A cell development phenotype related to the development of an akinete, a thick-walled dormant cell derived from the enlargement of a vegetative cell. OMP:MCC doi:10.1046/j.1469-8137.1999.00505.x endospore formation phenotype 2011-02-02T03:25:29Z A sporulation phenotype where development concerns formation of an endospore, a dormant, highly resistant spore with a thick wall that forms within the mother cell. FAO:0000019 GO:0034301 OMP:0000094 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype spore FAO:0000019 A sporulation phenotype where development concerns formation of an endospore, a dormant, highly resistant spore with a thick wall that forms within the mother cell. OMP:MCC endospore formation GO:0034301 spore germination phenotype 2011-02-02T03:25:47Z A cell development phenotype regarding the physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall). GO:0009847 OMP:0000095 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype spore germination GO:0009847 A cell development phenotype regarding the physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall). OMP:MCC myxospore formation phenotype 2011-02-02T03:26:41Z A sporulation phenotype related to development of a myxospore, a differentiated, resting cell usually within a fruiting body by Myxobacteria. GO:0034303 OMP:0000096 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne microbial_phenotype A sporulation phenotype related to development of a myxospore, a differentiated, resting cell usually within a fruiting body by Myxobacteria. OMP:MCC myxospore formation GO:0034303 absence of chemotaxis 2011-02-02T03:28:13Z A chemotaxis phenotype where a motile microbe doesn't display directed movement in response to a specific chemical concentration gradient. OMP:0000097 adrienne microbial_phenotype A chemotaxis phenotype where a motile microbe doesn't display directed movement in response to a specific chemical concentration gradient. OMP:MCC altered virulence 2011-04-28T02:11:35Z A virulence phenotype where the rate, frequency, time, or extent of the ability of a microbe to cause disease in another organism (host) is altered relative to a designated control. OMP:0000098 PATO:0002146 compatible interaction mchibucos microbial_phenotype virulence A virulence phenotype where the rate, frequency, time, or extent of the ability of a microbe to cause disease in another organism (host) is altered relative to a designated control. OMP:MCC hemolysis test 2011-06-07T03:17:22Z A differential test phenotype that describes whether a cell or cells exhibits the ability to lyse red blood cells. OMP:0000099 mchibucos microbial_phenotype A differential test phenotype that describes whether a cell or cells exhibits the ability to lyse red blood cells. OMP:WAM colony morphology phenotype 2011-02-02T02:14:39Z A multicellular phenotype dealing with the physical characteristics of an assemblage of microorganisms growing on a solid surface such as the surface of an agar culture medium. APO:0000060 Adrienne OMP:0000100 colony appearance phenotype microbial_phenotype A multicellular phenotype dealing with the physical characteristics of an assemblage of microorganisms growing on a solid surface such as the surface of an agar culture medium. ISBN:9780073302089 OMP:WAM colony appearance APO:0000060 microbial communication phenotype 2011-02-07T03:45:44Z A multi-organism phenotype where microbial organisms communicate and coordinate their activities through chemical signals that either diffuse through the environment or remain cell associated. Adrienne OMP:0000101 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A multi-organism phenotype where microbial organisms communicate and coordinate their activities through chemical signals that either diffuse through the environment or remain cell associated. OMP:JCH colony opacity phenotype 2011-06-07T12:18:14Z A colony morphology phenotype dealing with the degree to which light can pass through a colony. OMP:0000102 mchibucos microbial_phenotype A colony morphology phenotype dealing with the degree to which light can pass through a colony. OMP:WAM colony form phenotype 2011-02-02T02:41:50Z A colony morphology phenotype dealing with the basic shape or form of a colony or colonies. Adrienne OMP:0000103 microbial_phenotype A colony morphology phenotype dealing with the basic shape or form of a colony or colonies. OMP:WAM colony elevation phenotype 2011-02-02T02:42:12Z A colony morphology phenotype dealing with the height or vertical growth of the colony. Adrienne OMP:0000104 microbial_phenotype A colony morphology phenotype dealing with the height or vertical growth of the colony. OMP:WAM aerotolerant anaerobe 2011-06-06T03:43:38Z A microbial phenotype that describes a microorganism that does not require oxygen gas (O2) for growth and doesn't utilize O2 even when it is present. OMP:0000105 mchibucos microbial_phenotype A microbial phenotype that describes a microorganism that does not require oxygen gas (O2) for growth and doesn't utilize O2 even when it is present. ISBN:9780073402406 OMP:WAM colony sheen phenotype 2011-02-02T02:42:37Z A colony surface phenotype characterized by a soft luster on the surface. Adrienne OMP:0000106 microbial_phenotype A colony surface phenotype characterized by a soft luster on the surface. OMP:JCH colony pigmentation phenotype 2011-02-02T02:43:25Z A colony morphology phenotype related to the color of a colony or colonies. Adrienne OMP:0000107 microbial_phenotype A colony morphology phenotype related to the color of a colony or colonies. OMP:WAM colony optical phenotype 2011-02-02T02:43:46Z A colony morphology phenotype dealing with the interaction of a colony or colonies and light. Adrienne OMP:0000108 microbial_phenotype A colony morphology phenotype dealing with the interaction of a colony or colonies and light. OMP:JCH presence of mucoid colonies 2011-02-07T03:38:08Z A mucoid colony phenotype where the colonies are mucoid. Adrienne OMP:0000109 microbial_phenotype viscous colony texture A mucoid colony phenotype where the colonies are mucoid. ISBN:1555810489 OMP:WAM OMP:WAM viscous colony texture opaque colony 2011-02-02T02:45:02Z A colony opacity phenotype characterized by inability of light to pass through it. Adrienne OMP:0000110 SNOMED:P3-51350 microbial_phenotype A colony opacity phenotype characterized by inability of light to pass through it. OMP:WAM presence of motility by swimming 2011-02-07T03:17:40Z A presence of motility phenotype where a microbe exhibits smooth movement through a liquid medium. In Bacteria and Archaea, motility by swimming is typically powered by a flagellum or flagella. In Protists, swimming motility is typically powered by cilia or flagella. OMP:0000111 adrienne microbial_phenotype A presence of motility phenotype where a microbe exhibits smooth movement through a liquid medium. OMP:MCC presence of motility by gliding 2011-02-07T03:18:03Z A presence of motility phenotype where a microbe exhibits smooth movement along a solid surface. OMP:0000112 adrienne microbial_phenotype A presence of motility phenotype where a microbe exhibits smooth movement along a solid surface. OMP:MCC presence of motility by twitching 2011-02-07T03:18:13Z A presence of motility phenotype where a microbe exhibits movement over moist surfaces by the extension, tethering, and then retraction of polar pili. GO:0043107 OMP:0000113 Twitching motility of bacteria typically involves type IV pili. adrienne microbial_phenotype A presence of motility phenotype where a microbe exhibits movement over moist surfaces by the extension, tethering, and then retraction of polar pili. OMP:MCC PMID:12142488 type IV pilus-dependent motility GO:0043107 translucent colony 2011-02-02T02:45:20Z A colony opacity phenotype characterized by an almost clear but distorted, frosted glass appearance. Adrienne OMP:0000114 SNOMED:P3-51370 microbial_phenotype semi-translucent A colony opacity phenotype characterized by an almost clear but distorted, frosted glass appearance. OMP:WAM transparent colony 2011-02-02T02:45:41Z A colony opacity phenotype characterized by a clear appearance. Adrienne OMP:0000115 SNOMED:P3-51360 microbial_phenotype A colony opacity phenotype characterized by a clear appearance. OMP:WAM pigmented colony 2011-02-02T02:46:17Z A colony pigmentation phenotype where colonies are pigmented. Adrienne OMP:0000116 microbial_phenotype A colony pigmentation phenotype where colonies are pigmented. OMP:WAM diplococcus 2011-02-18T02:29:12Z A cell arrangement phenotype where an organism forms pairs of coccus cells, which arise from a division event in one plane. OMP:0000117 adrienne microbial_phenotype A cell arrangement phenotype where an organism forms pairs of coccus cells, which arise from a division event in one plane. ISBN:9780073402406 OMP:AEZ streptococcus 2011-02-18T02:31:37Z A cell arrangement phenotype where chains of coccus cells arise from division events in one plane. OMP:0000118 adrienne microbial_phenotype A cell arrangement phenotype where chains of coccus cells arise from division events in one plane. OMP:AEZ tetrad 2011-02-18T02:33:22Z A cell arrangement phenotype where squares of four coccus cells arise from division in two planes. OMP:0000119 adrienne microbial_phenotype micrococcus arrangement A cell arrangement phenotype where squares of four coccus cells arise from division in two planes. OMP:AEZ sarcina 2011-02-18T02:34:40Z A cell arrangement phenotype where cubes of eight coccus cells arise from a division event in three planes. OMP:0000120 adrienne microbial_phenotype A cell arrangement phenotype where cubes of eight coccus cells arise from a division event in three planes. OMP:AEZ staphylococcus 2011-02-18T02:39:34Z A cell arrangement phenotype where irregular clumps of coccus cells arise from division events in random planes. OMP:0000121 adrienne microbial_phenotype A cell arrangement phenotype where irregular clumps of coccus cells arise from division events in random planes. OMP:AEZ streptobacillus 2011-02-18T02:47:10Z A cell arrangement phenotype where bacillis cells are arranged in chains. OMP:0000122 adrienne microbial_phenotype A cell arrangement phenotype where bacillis cells are arranged in chains. OMP:AEZ coccobacillus cell shape 2011-02-18T02:48:21Z A cell shape phenotype where a cell is intermediate in shape between a coccus (sphere) and a bacillus (rod). OMP:0000123 adrienne microbial_phenotype A cell shape phenotype where a cell is intermediate in shape between a coccus (sphere) and a bacillus (rod). ISBN:9780073402406 OMP:MCC spirillum 2011-02-18T02:51:54Z A spiral cell shape phenotype where a cell forms a rigid spiral. OMP:0000124 adrienne microbial_phenotype A spiral cell shape phenotype where a cell forms a rigid spiral. ISBN:9780073402406 OMP:AEZ spirochete 2011-02-18T02:52:33Z A spiral cell shape phenotype where a cell forms a flexible spiral. OMP:0000125 adrienne microbial_phenotype A spiral cell shape phenotype where a cell forms a flexible spiral. ISBN:9780073402406 OMP:AEZ trichome-forming 2011-02-18T02:55:59Z A cell arrangement phenotype that consists of chains of cells in which the individual cells, which are usually wider than long, are closely appressed for the whole or the greater part of their width. OMP:0000126 adrienne microbial_phenotype A cell arrangement phenotype that consists of chains of cells in which the individual cells, which are usually wider than long, are closely appressed for the whole or the greater part of their width. OMP:DAS PMID:5318446 sheathed 2011-02-18T02:59:18Z A cell arrangement phenotype where chains of cells are enclosed in a hyaline envelope or sheath. OMP:0000127 adrienne microbial_phenotype A cell arrangement phenotype where chains of cells are enclosed in a hyaline envelope or sheath. OMP:MCC stalked cell shape 2011-02-18T02:59:38Z A cell shape phenotype where a cell possesses an appendage called a stalk or prostheca (plural, prosthecae), which is a tubular extension of the cell envelope and contains cytosol. OMP:0000128 adrienne microbial_phenotype prosthecate bacterium URL:http://en.wikipedia.org/wiki/Prosthecate_bacteria prosthecate bacterium A cell shape phenotype where a cell possesses an appendage called a stalk or prostheca (plural, prosthecae), which is a tubular extension of the cell envelope and contains cytosol. OMP:MCC PMID:14245437 cuboidal cell shape 2011-02-18T02:59:57Z A cell shape phenotype where a cell has a cube-like shape; there are six sides and the width is approximately equal to the height of the cell. OMP:0000129 adrienne microbial_phenotype square A cell shape phenotype where a cell has a cube-like shape; there are six sides and the width is approximately equal to the height of the cell. OMP:MCC star-shaped cell shape 2011-02-18T03:00:30Z A cell shape phenotype where a cell has projections that form points. OMP:0000130 adrienne microbial_phenotype A cell shape phenotype where a cell has projections that form points. OMP:MCC lobed cell shape 2011-02-18T03:00:58Z A cell shape phenotype where a cell has curved or rounded projections or divisions (lobes). OMP:0000131 PATO:0001979 adrienne microbial_phenotype A cell shape phenotype where a cell has curved or rounded projections or divisions (lobes). OMP:MCC lobed PATO:0001979 pleomorphic cell shape 2011-02-18T03:01:18Z A cell shape phenotype where a cell is variable in shape and lacks a single, characteristic form. OMP:0000132 PATO:0001356 adrienne microbial_phenotype A cell shape phenotype where a cell is variable in shape and lacks a single, characteristic form. ISBN:9780073402406 OMP:MCC absence of motility 2011-02-18T03:33:32Z A motility phenotype where a microbe lacks the ability to perform controlled self-propelled movement that results in translocation of the cell from one place to another. OMP:0000133 adrienne microbial_phenotype non-motile A motility phenotype where a microbe lacks the ability to perform controlled self-propelled movement that results in translocation of the cell from one place to another. OMP:MCC spherical akinete 2011-02-18T03:40:27Z An akinete morphology phenotype where the organism forms a spherical akinete. OMP:0000134 adrienne microbial_phenotype An akinete morphology phenotype where the organism forms a spherical akinete. OMP:JCH akinete envelope attribute 2011-02-18T03:41:16Z An akinete formation phenotype where the traits described are from the cells thick-walled outer membrane. OMP:0000135 adrienne microbial_phenotype An akinete formation phenotype where the traits described are from the cells thick-walled outer membrane. OMP:JCH in vitro nucleoid shape 2011-02-21T04:16:30Z A nucleoid phenotype dealing with shape of the nucleoid region. OMP:0000136 adrienne microbial_phenotype A nucleoid phenotype dealing with shape of the nucleoid region. OMP:WAM non-pigmented colony 2011-02-02T02:46:39Z A colony pigmentation phenotype colonies are non-pigmented. Adrienne OMP:0000137 colorless colony microbial_phenotype A colony pigmentation phenotype colonies are non-pigmented. OMP:WAM altered cell circularity variability 2020-07-22T22:32:45Z Cell circularity is defined as (2*pi*cell area/(cell perimeter)^2). OMP:0000138 microbial_phenotype siegele dull colony sheen 2011-02-02T02:47:21Z A colony form phenotype characterized by a dull luster on the surface. Adrienne OMP:0000139 SNOMED:P3-513150 matte microbial_phenotype rough A colony form phenotype characterized by a dull luster on the surface. OMP:JCH nucleoid spacing 2011-02-21T04:25:41Z A nucleoid phenotype that describes the distribution of within a cell or cells. OMP:0000140 adrienne microbial_phenotype A nucleoid phenotype that describes the distribution of within a cell or cells. OMP:AZ regular nucleoid spacing 2011-02-21T04:26:57Z A nucleoid spacing phenotype where multiple nucleoids within a single cell exhibit regular spacing. OMP:0000141 adrienne microbial_phenotype A nucleoid spacing phenotype where multiple nucleoids within a single cell exhibit regular spacing. OMP:AZ irregular nucleoid spacing 2011-02-21T04:27:22Z A nucleoid spacing phenotype where multiple nucleoids within a single cell exhibit irregular spacing. OMP:0000142 adrienne microbial_phenotype A nucleoid spacing phenotype where multiple nucleoids within a single cell exhibit irregular spacing. OMP:AZ single nucleoid 2011-02-21T04:27:48Z A nucleoid number phenotype where there is only one nucleoid region in the cell. OMP:0000143 adrienne microbial_phenotype A nucleoid number phenotype where there is only one nucleoid region in the cell. OMP:WAM multiple nucleoids 2011-02-21T04:28:30Z A nucleoid number phenotype where there is more than one nucleoid regions in the cell. OMP:0000144 adrienne microbial_phenotype A nucleoid number phenotype where there is more than one nucleoid regions in the cell. OMP:WAM nucleoid localization 2011-02-21T04:30:32Z A nucleoid phenotype that describes the location of the nucleoid within a cell or cells. OMP:0000145 adrienne microbial_phenotype A nucleoid phenotype that describes the location of the nucleoid within a cell or cells. OMP:JCH midcell nucleoid localization 2011-02-21T04:31:22Z A nucleoid localization phenotype where the nucleoid is localized at the center of the cell. OMP:0000146 adrienne microbial_phenotype A nucleoid localization phenotype where the nucleoid is localized at the center of the cell. OMP:WAM polar nucleoid localization 2011-02-21T04:31:46Z A nucleoid localization phenotype where the nucleoid is located in one of the polar regions of the cell. OMP:0000147 adrienne microbial_phenotype A nucleoid localization phenotype where the nucleoid is located in one of the polar regions of the cell. OMP:WAM quarter cell nucleoid localization 2011-02-21T04:32:04Z A nucleoid localization phenotype where the nucleoid is localized midway between the pole and midpoint of a cell. OMP:0000148 adrienne microbial_phenotype A nucleoid localization phenotype where the nucleoid is localized midway between the pole and midpoint of a cell. OMP:AZ colony margin phenotype 2011-02-02T02:47:43Z A colony morphology phenotype dealing with the shape of the edge of a colony viewed with magnification. Adrienne OMP:0000149 microbial_phenotype A colony morphology phenotype dealing with the shape of the edge of a colony viewed with magnification. OMP:WAM nucleoid phenotype 2011-02-21T04:36:21Z A genetic material phenotype where the trait in question is the nucleoid, the region of a bacterial or archaeal cell to which the DNA is confined. OMP:0000150 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. adrienne genophore microbial_phenotype A genetic material phenotype where the trait in question is the nucleoid, the region of a bacterial or archaeal cell to which the DNA is confined. OMP:MCC entire margin 2011-02-02T02:47:59Z A colony margin phenotype characterized by smooth growth, with no projections along the edge. Adrienne OMP:0000151 SNOMEDCT:12774002 microbial_phenotype A colony margin phenotype characterized by smooth growth, with no projections along the edge. OMP:WAM doublet nucleoid 2011-02-22T02:27:29Z A nucleoid shape phenotype where the nucleoid isolated from a cell is shaped like a dumbbell. OMP:0000152 adrienne dumbbell nucleoid microbial_phenotype OMP:WAM dumbbell nucleoid A nucleoid shape phenotype where the nucleoid isolated from a cell is shaped like a dumbbell. OMP:WAM singlet nucleoid 2011-02-22T02:27:58Z A nucleoid shape phenotype where the nucleoid isolated from a cell is compacted. OMP:0000153 adrienne microbial_phenotype A nucleoid shape phenotype where the nucleoid isolated from a cell is compacted. OMP:WAM undulate margin 2011-02-02T02:48:11Z A colony margin phenotype characterized by wavy growth along the colony edge. Adrienne OMP:0000154 SNOMEDCT:48408000 microbial_phenotype A colony margin phenotype characterized by wavy growth along the colony edge. OMP:WAM Bacterial colony morphology, undulate margin SNOMEDCT:48408000 lobate margin 2011-02-02T02:48:33Z A colony margin phenotype characterized by lobed growth along the colony edge. Adrienne OMP:0000155 SNOMEDCT:36580002 microbial_phenotype A colony margin phenotype characterized by lobed growth along the colony edge. OMP:WAM erose margin 2011-02-02T02:48:46Z A colony margin phenotype characterized by growth that appears jagged or zig-zagged along the edge of the colony. Adrienne OMP:0000156 SNOMEDCT:86734000 microbial_phenotype A colony margin phenotype characterized by growth that appears jagged or zig-zagged along the edge of the colony. OMP:WAM filiform margin 2011-02-02T02:49:05Z A colony margin phenotype characterized by thread or filamentous shaped edge. Adrienne OMP:0000157 SNOMEDCT:42844005 filamentous margin microbial_phenotype A colony margin phenotype characterized by thread or filamentous shaped edge. OMP:JCH Bacterial colony morphology, filamentous margin SNOMEDCT:42844005 curled margin 2011-02-02T02:49:30Z A colony margin phenotype characterized by growth that appears as waves or curls along the edge of the colony. Adrienne OMP:0000158 SNOMEDCT:85764001 microbial_phenotype A colony margin phenotype characterized by growth that appears as waves or curls along the edge of the colony. OMP:JCH absence of aerotaxis 2011-03-02T02:06:09Z An aerotaxis phenotype where a motile microbe doesn't display directed movement in response to environmental oxygen (O2). OMP:0000159 adrienne microbial_phenotype An aerotaxis phenotype where a motile microbe doesn't display directed movement in response to environmental oxygen (O2). OMP:MCC flat colony elevation 2011-02-02T02:49:49Z A colony elevation phenotype characterized by no growth above the medium. Adrienne OMP:0000160 SNOMED:P3-51130 microbial_phenotype A colony elevation phenotype characterized by no growth above the medium. OMP:WAM raised colony elevation 2011-02-02T02:50:01Z A colony elevation phenotype characterized by uniform growth above the medium. Adrienne OMP:0000161 SNOMED:P3-51140 microbial_phenotype A colony elevation phenotype characterized by uniform growth above the medium. OMP:WAM convex colony elevation 2011-02-02T02:50:11Z A colony elevation phenotype characterized by sloping up from the edges. Adrienne OMP:0000162 SNOMEDCT:26875006 microbial_phenotype A colony elevation phenotype characterized by sloping up from the edges. OMP:WAM Bacterial colony elevation, convex SNOMEDCT:26875006 pulvinate colony elevation 2011-02-02T02:50:30Z A colony elevation phenotype characterized by sloping steeply from edges and very high in the center. Adrienne OMP:0000163 microbial_phenotype A colony elevation phenotype characterized by sloping steeply from edges and very high in the center. OMP:WAM umbonate colony elevation 2011-02-02T02:50:42Z A colony elevation phenotype characterized by raised growth in the center. Adrienne OMP:0000164 SNOMEDCT:70929009 microbial_phenotype Bacterial colony elevation, umbonate SNOMEDCT:70929009 A colony elevation phenotype characterized by raised growth in the center. OMP:WAM increased colony size 2011-06-07T01:55:00Z A colony size phenotype where colony size is increased relative to a designated control. OMP:0000165 mchibucos microbial_phenotype A colony size phenotype where colony size is increased relative to a designated control. OMP:JCH circular colony 2011-02-02T02:51:18Z A colony form phenotype characterized by growth in a round shape. Adrienne OMP:0000166 SNOMEDCT:64781005 microbial_phenotype A colony form phenotype characterized by growth in a round shape. OMP:WAM irregular colony 2011-02-02T02:51:35Z A colony form phenotype characterized by growth without a defined shape or size. Adrienne OMP:0000167 SNOMEDCT:39696006 microbial_phenotype A colony form phenotype characterized by growth without a defined shape or size. OMP:WAM rhizoid colony 2011-02-02T02:51:57Z A colony form phenotype characterized by the growth of thin, branching projections. Adrienne OMP:0000168 SNOMEDCT:113047000 microbial_phenotype A colony form phenotype characterized by the growth of thin, branching projections. OMP:WAM spindle colony 2011-02-02T02:52:30Z A colony form phenotype characterized by growth being wide in the middle then tapering at both ends. Adrienne OMP:0000169 SNOMEDCT:77324006 microbial_phenotype A colony form phenotype characterized by growth being wide in the middle then tapering at both ends. OMP:JCH decreased cell circularity variability 2020-07-22T22:34:00Z OMP:0000170 microbial_phenotype siegele microaerophile 2011-06-06T03:44:11Z An oxygen growth range phenotype where growth and reproduction requires oxygen but at levels below that found in air (approx. 21%). A microbial phenotype that describes a microorganism that requires O2 for growth, but doesn't grow in the presence of atmospheric levels of O2. Optimal growth of a microaerophile occurs in environments with xx% - xx% O2. OMP:0000171 Optimal oxygen levels for growth of typical microaerophilic bacteria is 2 to 10% O2, and growth is impaired by atmospheric oxygen levels (approx. 21%). mchibucos microbial_phenotype An oxygen growth range phenotype where growth and reproduction requires oxygen but at levels below that found in air (approx. 21%). A microbial phenotype that describes a microorganism that requires O2 for growth, but doesn't grow in the presence of atmospheric levels of O2. Optimal growth of a microaerophile occurs in environments with xx% - xx% O2. ISBN:9780073402406 OMP:WAM response to chemical stimulus phenotype 2011-06-06T04:16:08Z A stress response phenotype dealing with the response to exposure to chemical stimuli. OMP:0000172 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A stress response phenotype dealing with the response to exposure to chemical stimuli. OMP:WAM response to stress phenotype 2011-02-02T03:13:32Z A biological process phenotype related to a change in state or activity of a microbe (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). Adrienne OMP:0000173 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A biological process phenotype related to a change in state or activity of a microbe (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). FYPO:0002549 GO:0006950 OMP:WAM growth phenotype 2011-02-02T03:13:59Z A microbial phenotype related to the increase in size or mass over time of an entire organism, a part of an organism, or a cell. Adrienne GO:0040007 OMP:0000174 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. For phenotypes affecting growth of a population, see OMP:0007167 ! population growth phenotype. microbial_phenotype growth GO:0040007 A microbial phenotype related to the increase in size or mass over time of an entire organism, a part of an organism, or a cell. GO:0040007 OMP:WAM nanotube phenotype 2011-06-07T02:59:54Z A cell projection phenotype where the structure in question is a tube. OMP:0000175 mchibucos microbial_phenotype A cell projection phenotype where the structure in question is a tube. OMP:DAS biofilm formation phenotype 2011-02-02T03:17:19Z A multi-organism phenotype dealing with the process in which microorganisms attach to and grow on a surface and produce extracellular polymers that facilitate attachment and matrix formation. Adrienne OMP:0000176 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A multi-organism phenotype dealing with the process in which microorganisms attach to and grow on a surface and produce extracellular polymers that facilitate attachment and matrix formation. GO:0042710 OMP:WAM liquid culture morphology phenotype 2011-02-02T03:20:39Z A growth phenotype dealing with the morphological characteristics of a culture growing in a liquid medium. APO:0000064 Adrienne OMP:0000177 microbial_phenotype liquid culture appearance APO:0000064 A growth phenotype dealing with the morphological characteristics of a culture growing in a liquid medium. OMP:WAM flocculation phenotype 2011-02-02T03:21:00Z A liquid culture morphology phenotype where cells aggregate together in suspension to form clumps of many cells known as flocs. APO:0000065 Adrienne OMP:0000178 clumping flocculation microbial_phenotype flocculation APO:0000065 A liquid culture morphology phenotype where cells aggregate together in suspension to form clumps of many cells known as flocs. GO:0000128 ISBN:9780763743031 OMP:WAM colony size phenotype 2011-02-02T03:22:43Z A colony morphology phenotype dealing with the size of the colony. Adrienne OMP:0000179 microbial_phenotype A colony morphology phenotype dealing with the size of the colony. OMP:WAM metabolic phenotype 2011-06-06T03:59:59Z A microbial phenotype that deals with the chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolism OMP:0000180 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A microbial phenotype that deals with the chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. GO:0008152 colony with diffusible pigment 2011-06-07T12:18:54Z A colony pigmentation phenotype characterized by the presence of diffusible/water soluble pigments that color the agar around the colony. OMP:0000181 mchibucos microbial_phenotype A colony pigmentation phenotype characterized by the presence of diffusible/water soluble pigments that color the agar around the colony. OMP:WAM gas production test 2011-02-07T03:52:30Z A differential test phenotype that describes ability of an organism to produce a gas, such as CO2, as the result of metabolic activities during growth. Adrienne OMP:0000182 microbial_phenotype A differential test phenotype that describes ability of an organism to produce a gas, such as CO2, as the result of metabolic activities during growth. OMP:JCH anaerobic respiration with sulfate as the terminal acceptor 2011-02-07T03:52:44Z A presence of anaerobic respiration phenotype where sulfate (SO4) is used as the terminal electron acceptor. Adrienne GO:0019420 OMP:0000183 dissimilatory sulfate reduction microbial_phenotype sulfide production ISBN:978-0-07-340240-6 dissimilatory sulfate reduction dissimilatory sulfate reduction GO:0019420 A presence of anaerobic respiration phenotype where sulfate (SO4) is used as the terminal electron acceptor. ISBN:978-0-07-340240-6 OMP:DAS obligate anaerobe 2011-02-02T03:29:34Z A microbial phenotype that describes a microorganism that does not grow in the presence of oxygen gas (O2). Adrienne OMP:0000184 microbial_phenotype strict anaerobe A microbial phenotype that describes a microorganism that does not grow in the presence of oxygen gas (O2). ISBN:9780073402406 OMP:WAM obligate aerobe 2011-02-02T03:29:51Z A microbial phenotype that describes a microorganism that requires the presence of oxygen gas (O2) for growth. Adrienne OMP:0000185 microbial_phenotype strict aerobe A microbial phenotype that describes a microorganism that requires the presence of oxygen gas (O2) for growth. ISBN:9780073402406 OMP:WAM increased cell circularity variability 2020-07-22T22:34:00Z OMP:0000186 microbial_phenotype siegele granulation phenotype 2011-06-07T02:22:14Z A liquid culture morphology phenotype where cells group together and form small particles in the medium. OMP:0000187 granulation in liquid mchibucos microbial_phenotype precipitation in liquid culture A liquid culture morphology phenotype where cells group together and form small particles in the medium. ISBN:9780763743031 OMP:WAM gram positive 2011-02-02T03:34:29Z A gram stain phenotype where a cell or cells retain crystal violet stain when decolorized with an organic solvent such as ethanol. Adrienne GO:0009275 OMP:0000188 microbial_phenotype Gram-positive-bacterium-type cell wall GO:0009275 A gram stain phenotype where a cell or cells retain crystal violet stain when decolorized with an organic solvent such as ethanol. OMP:DAS gram negative 2011-02-02T03:34:45Z A gram stain phenotype where a cell or cells do not retain crystal violet stain when decolorized with an organic solvent such as ethanol. Adrienne GO:0009276 OMP:0000189 microbial_phenotype A gram stain phenotype where a cell or cells do not retain crystal violet stain when decolorized with an organic solvent such as ethanol. OMP:DAS Gram-negative-bacterium-type cell wall GO:0009276 gram variable 2011-02-02T03:34:58Z A gram stain phenotype where a cell or cells give variable results to the gram stain. Adrienne OMP:0000190 microbial_phenotype A gram stain phenotype where a cell or cells give variable results to the gram stain. OMP:DAS gram stain phenotype 2011-02-02T03:35:15Z A cell staining phenotype where microorganisms are grouped based on their ability to retain crystal violet stain when decolorized with an organic solvent such as ethanol. Adrienne OMP:0000191 SNOMEDCT:385484003 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A cell staining phenotype where microorganisms are grouped based on their ability to retain crystal violet stain when decolorized with an organic solvent such as ethanol. ISBN:978-0-07-340240-6 ISBN:978-0077292812 OMP:DAS Gram stain SNOMEDCT:385484003 chemical production phenotype 2011-02-03T11:24:08Z A metabolic phenotype that deals with the chemical reactions and pathways resulting in the formation of chemicals. Adrienne OMP:0000192 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A metabolic phenotype that deals with the chemical reactions and pathways resulting in the formation of chemicals. OMP:JCH altered cell aspect ratio 2020-07-22T22:35:03Z An altered cell shape phenotype where the cell aspect ratio (cell diameter/cell length) of a microbial cell is altered relative to a designated control. OMP:0000193 microbial_phenotype siegele An altered cell shape phenotype where the cell aspect ratio (cell diameter/cell length) of a microbial cell is altered relative to a designated control. OMP:das catalase positive 2011-06-06T04:28:49Z A catalase test phenotype where an organism exhibits catalase activity. OMP:0000194 mchibucos microbial_phenotype A catalase test phenotype where an organism exhibits catalase activity. OMP:JCH decreased catalase activity 2011-06-06T04:29:20Z An altered catalase activity phenotype where catalase activity is decreased relative to a designated control. OMP:0000195 mchibucos microbial_phenotype An altered catalase activity phenotype where catalase activity is decreased relative to a designated control. OMP:JCH increased catalase activity 2011-06-06T04:29:39Z An altered catalase activity phenotype where catalase activity is increased relative to a designated control. OMP:0000196 mchibucos microbial_phenotype positive regulation of catalase activity GO:1902553 positive regulation of catalase activity An altered catalase activity phenotype where catalase activity is increased relative to a designated control. OMP:JCH microbe-host interaction phenotype 2011-02-03T11:25:01Z A microbial phenotype related to the interactions between a microbe and its host(s). APO:0000287 Adrienne GO:0051704 OMP:0000197 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A microbial phenotype related to the interactions between a microbe and its host(s). OMP:WAM interaction with host/environment APO:0000287 multi-organism process GO:0051704 catalase negative 2011-06-06T04:30:12Z A catalase test phenotype where an organism doesn't exhibit catalase activity. OMP:0000198 mchibucos microbial_phenotype A catalase test phenotype where an organism doesn't exhibit catalase activity. OMP:JCH acid-fast staining phenotype 2011-02-03T11:38:46Z A cell-staining phenotype where a cell or cells are classified based on whether they are decolorized by an acid-alcohol mixture after staining, typically with carbolfuchsin. Adrienne OMP:0000199 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A cell-staining phenotype where a cell or cells are classified based on whether they are decolorized by an acid-alcohol mixture after staining, typically with carbolfuchsin. ISBN:978-0-07-729281-1 OMP:DAS colony with non-diffusible pigment 2011-06-07T12:19:32Z A colony pigmentation phenotype characterized by pigmentation only in the colony. OMP:0000200 mchibucos microbial_phenotype A colony pigmentation phenotype characterized by pigmentation only in the colony. OMP:WAM nanotube mediated communication 2011-03-02T01:41:52Z A microbial communication phenotype communication is facilitated between one or more microbes by a connected nanotube. Adrienne OMP:0000201 microbial_phenotype nanotubule mediated communication A microbial communication phenotype communication is facilitated between one or more microbes by a connected nanotube. OMP:WAM PMID:21335240 outer membrane vesicles phenotype 2011-03-02T01:43:12Z A cell envelope phenotype that describes the ability of a cell or cells to produce outer membrane vesicles. Adrienne OMP:0000202 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A cell envelope phenotype that describes the ability of a cell or cells to produce outer membrane vesicles. OMP:JCH PMID:20825345 capsule phenotype 2011-06-07T09:44:51Z A cell envelope phenotype where the trait in question is the capsule, a layer of polysaccharide or poly-amino acids surrounding a microbial cell. When present, the capsule is the outermost layer of the cell envelope. APO:0000331 OMP:0000203 glycocalyx mchibucos microbial_phenotype slime layer capsule formation APO:0000331 A cell envelope phenotype where the trait in question is the capsule, a layer of polysaccharide or poly-amino acids surrounding a microbial cell. When present, the capsule is the outermost layer of the cell envelope. ISBN:9780073402406 OMP:DAS presence of capsule 2011-06-07T09:45:20Z A capsule phenotype where a cell or cells have a capsule. OMP:0000204 When present, the capsule layer lies outside the cell wall and/or outer membrane. glycocalyx mchibucos microbial_phenotype slime layer OMP:DAS slime layer OMP:DAS glycocalyx A capsule phenotype where a cell or cells have a capsule. OMP:DAS forms single species biofilm 2011-06-07T02:26:30Z A biofilm phenotype where the biofilm is formed by a single species. OMP:0000205 mchibucos microbial_phenotype A biofilm phenotype where the biofilm is formed by a single species. OMP:WAM altered hemolysis test result 2011-06-07T03:17:46Z A hemolysis test phenotype where the ability to cause hemolysis is altered relative to a designated control. OMP:0000206 mchibucos microbial_phenotype A hemolysis test phenotype where the ability to cause hemolysis is altered relative to a designated control. OMP:WAM serotype phenotype 2011-03-02T02:16:33Z A microbial phenotype that is distinguished by the presence a specific surface antigen. Adrienne OMP:0000207 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. antigenic typing phenotype microbial_phenotype serological test phenotype serovar A microbial phenotype that is distinguished by the presence a specific surface antigen. OMP:MCC absence of hemolysis 2011-06-07T03:18:33Z A hemolysis test phenotype where a cell or cells does not cause hemolysis. OMP:0000208 mchibucos microbial_phenotype A hemolysis test phenotype where a cell or cells does not cause hemolysis. OMP:WAM fluorescent colony 2011-06-07T12:20:31Z A colony pigmentation phenotype where the prominent morphological characteristic of the colony(ies) is the presence of fluorescence. OMP:0000209 mchibucos microbial_phenotype A colony pigmentation phenotype where the prominent morphological characteristic of the colony(ies) is the presence of fluorescence. OMP:WAM colony surface phenotype 2011-06-07T12:31:24Z A colony morphology phenotype that describes the appearance of the surface of a colony or colonies. OMP:0000210 mchibucos microbial_phenotype A colony morphology phenotype that describes the appearance of the surface of a colony or colonies. OMP:WAM absence of capsule 2011-06-07T09:49:20Z A capsule phenotype where a cell or cells lack capsule. OMP:0000211 mchibucos microbial_phenotype A capsule phenotype where a cell or cells lack capsule. OMP:DAS smooth colony surface 2011-06-07T12:32:12Z A colony surface phenotype where colonies have a shiny glistening surface. OMP:0000212 SNOMEDCT:90926009 mchibucos microbial_phenotype Bacterial colony surface, smooth SNOMEDCT:90926009 A colony surface phenotype where colonies have a shiny glistening surface. ISBN:1555810489 OMP:WAM increased number of flagella 2011-06-07T09:53:17Z An altered flagellum phenotype where the number of flagella per cell is increased relative to a designated control. OMP:0000213 mchibucos microbial_phenotype An altered flagellum phenotype where the number of flagella per cell is increased relative to a designated control. OMP:DAS cell staining phenotype 2011-02-03T01:33:37Z A microbial phenotype where a cell or cells are treated with a dye or dyes for purposes of identification and classification. APO:0000061 Adrienne OMP:0000214 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A microbial phenotype where a cell or cells are treated with a dye or dyes for purposes of identification and classification. OMP:DAS colony color APO:0000061 decreased number of flagella 2011-06-07T09:54:51Z An altered flagellum phenotype where the number of flagella per cell is decreased relative to a designated control. OMP:0000215 mchibucos microbial_phenotype An altered flagellum phenotype where the number of flagella per cell is decreased relative to a designated control. OMP:DAS aerobic respiration phenotype 2011-02-07T03:53:18Z A respiration phenotype where oxygen (O2) is used as the terminal electron acceptor. Adrienne OMP:0000216 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A respiration phenotype where oxygen (O2) is used as the terminal electron acceptor. ISBN:978-0-07-340240-6 OMP:DAS increased hemolysis 2011-06-07T03:19:00Z An altered hemolysis phenotype where hemolysis is increased relative to a designated control. OMP:0000217 mchibucos microbial_phenotype An altered hemolysis phenotype where hemolysis is increased relative to a designated control. OMP:WAM catalase test phenotype 2011-02-03T04:43:28Z A differential test phenotype that relates to the presence or absence of catalase, an enzyme that catalyzes the decomposition of hydrogen peroxide into oxygen and water. Adrienne GO:0004096 OMP:0000218 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Catalysis of the reaction: 2 hydrogen peroxide = O2 + 2 H2O [EC:1.11.1.6]. microbial_phenotype catalase activity GO:0004096 A differential test phenotype that relates to the presence or absence of catalase, an enzyme that catalyzes the decomposition of hydrogen peroxide into oxygen and water. ISBN:9780895828309 OMP:JCH decarboxylase test phenotype 2011-02-03T04:43:53Z A differential test phenotype that describes the ability of an organism to catalyze the removal of a carboxyl group from an amino acid, typically lysine, ornithine, or arginine. Adrienne OMP:0000219 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A differential test phenotype that describes the ability of an organism to catalyze the removal of a carboxyl group from an amino acid, typically lysine, ornithine, or arginine. ISBN:9780895828309 OMP:JCH oxidase test phenotype 2011-02-03T04:44:11Z A differential test phenotype that relates to the presence or absence of cytochrome oxidase based on the ability of an organism to oxidize certain aromatic amines to form colored end products. Adrienne OMP:0000220 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A differential test phenotype that relates to the presence or absence of cytochrome oxidase based on the ability of an organism to oxidize certain aromatic amines to form colored end products. ISBN:9780895828309 OMP:JCH enzymatic activity phenotype 2011-02-03T04:44:39Z A microbial phenotype that affects an enzymatic activity. Enzymes are biological molecules that catalyze biochemical reactions at physiological temperatures. Enzymes possess specific binding sites for their substrates (reactants) and are usually composed wholly or largely of protein or RNA. Catalytic RNAs are also called ribozymes. Adrienne FYPO:0000654 GO:0003824 OMP:0000221 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. catalytic activity microbial_phenotype A microbial phenotype that affects an enzymatic activity. Enzymes are biological molecules that catalyze biochemical reactions at physiological temperatures. Enzymes possess specific binding sites for their substrates (reactants) and are usually composed wholly or largely of protein or RNA. Catalytic RNAs are also called ribozymes. ISBN:0198506732 OMP:JCH catalytic activity GO:0003824 catalytic activity phenotype FYPO:0000654 urease test phenotype 2011-02-03T04:45:37Z A differential test phenotype that relates to the presence or absence of urease, an enzyme that hydrolyzes urea to ammonia and carbon dioxide. Adrienne GO:0009039 OMP:0000222 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. microbial_phenotype A differential test phenotype that relates to the presence or absence of urease, an enzyme that hydrolyzes urea to ammonia and carbon dioxide. ISBN:9780895828309 OMP:JCH urease activity GO:0009039 decreased cell aspect ratio 2020-07-22T22:36:00Z An altered cell aspect ratio phenotype where the cell aspect ratio (cell diameter/cell length) of a microbial cell is decreased relative to a designated control. OMP:0000223 microbial_phenotype siegele An altered cell aspect ratio phenotype where the cell aspect ratio (cell diameter/cell length) of a microbial cell is decreased relative to a designated control. OMP:das energy metabolism phenotype 2011-06-06T04:53:09Z A metabolic phenotype that deals with the specific process an organism uses to produce energy carriers. OMP:0000224 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. bioenergetics mchibucos microbial_phenotype A metabolic phenotype that deals with the specific process an organism uses to produce energy carriers. OMP:JCH carbon dioxide production 2011-02-07T03:53:37Z A chemical production phenotype where carbon dioxide is produced. Adrienne OMP:0000225 microbial_phenotype A chemical production phenotype where carbon dioxide is produced. OMP:JCH increased cell aspect ratio 2020-07-22T22:36:00Z An altered cell aspect ratio phenotype where the cell aspect ratio (cell diameter/cell length) of a microbial cell is increased relative to a designated control. OMP:0000226 microbial_phenotype siegele An altered cell aspect ratio phenotype where the cell aspect ratio (cell diameter/cell length) of a microbial cell is increased relative to a designated control. OMP:das altered cell aspect ratio variability 2020-07-22T22:37:16Z OMP:0000227 microbial_phenotype siegele rough colony surface 2011-06-07T12:32:41Z A colony surface phenotype where a colony or colonies have a dull, bumpy, granular, or matte surface. OMP:0000228 SNOMEDCT:77092005 mchibucos microbial_phenotype Bacterial colony surface, rough SNOMEDCT:77092005 A colony surface phenotype where a colony or colonies have a dull, bumpy, granular, or matte surface. ISBN:1555810489 OMP:WAM colony consistency phenotype 2011-06-07T12:34:58Z A colony morphology phenotype that describes the consistency or texture of a colony or colonies when tested with a needle. OMP:0000229 colony texture mchibucos microbial_phenotype A colony morphology phenotype that describes the consistency or texture of a colony or colonies when tested with a needle. ISBN:1555810489 OMP:WAM rugose colony surface 2011-06-07T12:35:30Z A colony surface phenotype that is characterized by a surface that is wrinkled. OMP:0000230 mchibucos microbial_phenotype wrinkled colony surface A colony surface phenotype that is characterized by a surface that is wrinkled. OMP:JCH growth into medium 2011-06-07T12:38:26Z A colony elevation phenotype characterized by growth into the medium not above it. OMP:0000231 mchibucos microbial_phenotype A colony elevation phenotype characterized by growth into the medium not above it. OMP:WAM iridescent colony 2011-06-07T12:39:13Z A colony opacity phenotype characterized by varying colors being observed in reflected light. OMP:0000232 mchibucos microbial_phenotype A colony opacity phenotype characterized by varying colors being observed in reflected light. OMP:WAM decreased cell aspect ratio variability 2020-07-22T22:38:22Z OMP:0000233 microbial_phenotype siegele butyrous colony consistency 2011-06-07T12:41:24Z A colony consistency phenotype where a colony or colonies have a butter-like consistency. OMP:0000234 SNOMEDCT:25778006 buttery colony consistency mchibucos microbial_phenotype A colony consistency phenotype where a colony or colonies have a butter-like consistency. ISBN:1555810489 OMP:WAM Bacterial colony consistency, butyrous SNOMEDCT:25778006 increased cell aspect ratio variability 2020-07-22T22:38:22Z OMP:0000235 microbial_phenotype siegele dry colony consistency 2011-06-07T12:42:40Z A colony consistency phenotype where a colony or colonies have a brittle or powdery consistency. OMP:0000236 SNOMEDCT:87916001 friable colony mchibucos microbial_phenotype Bacterial colony consistency, friable SNOMEDCT:87916001 A colony consistency phenotype where a colony or colonies have a brittle or powdery consistency. ISBN:1555810489 OMP:WAM colony odor phenotype 2011-06-07T12:45:12Z A morphology phenotype dealing with the smell a colony produces. OMP:0000237 mchibucos microbial_phenotype A morphology phenotype dealing with the smell a colony produces. OMP:WAM crateriform colony elevation 2011-06-07T01:11:04Z A colony elevation phenotype characterized by crater like growth. OMP:0000238 mchibucos microbial_phenotype A colony elevation phenotype characterized by crater like growth. OMP:WAM plicate colony surface 2011-06-07T01:11:50Z A colony surface phenotype that is characterized by a surface arranged in parallel folds or ridges; pleated. OMP:0000239 mchibucos microbial_phenotype A colony surface phenotype that is characterized by a surface arranged in parallel folds or ridges; pleated. OMP:JCH punctiform colony 2011-06-07T01:50:03Z A colony form phenotype where a colony or colonies are small, but not microscopic, with a diameter of <1 mm. OMP:0000240 SNOMEDCT:55699002 mchibucos microbial_phenotype A colony form phenotype where a colony or colonies are small, but not microscopic, with a diameter of <1 mm. OMP:WAM decreased colony size 2011-06-07T01:55:22Z A colony size phenotype where colony size is decreased relative to a designated control. OMP:0000241 mchibucos microbial_phenotype A colony size phenotype where colony size is decreased relative to a designated control. OMP:JCH concentrically ringed surface colony 2011-06-07T01:58:00Z A colony surface phenotype characterized by rippled surface that radiate outward from a central point or axis. OMP:0000242 concentric colony surface texture mchibucos microbial_phenotype A colony surface phenotype characterized by rippled surface that radiate outward from a central point or axis. OMP:JCH sectored colony 2011-06-07T02:04:20Z A colony form phenotype characterized by the formation of wedged shaped sectors of varying colors and appearance in colonies growing on a solid substrate. OMP:0000243 mchibucos microbial_phenotype A colony form phenotype characterized by the formation of wedged shaped sectors of varying colors and appearance in colonies growing on a solid substrate. OMP:WAM papillated colony 2011-06-07T02:06:19Z A colony form phenotype characterized by growth of small, round or cone-shaped protuberances. OMP:0000244 colony papillation mchibucos microbial_phenotype A colony form phenotype characterized by growth of small, round or cone-shaped protuberances. OMP:JCH participates in multi-species biofilm 2011-06-07T02:27:00Z A biofilm phenotype where the formation involves two or more species. OMP:0000245 mchibucos microbial_phenotype A biofilm phenotype where the formation involves two or more species. OMP:WAM presence of nanotubes 2011-06-07T03:00:25Z A nanotube phenotype where a cell or cells have the ability to produce nanotubes. OMP:0000246 mchibucos microbial_phenotype A nanotube phenotype where a cell or cells have the ability to produce nanotubes. OMP:JCH absence of nanotubes 2011-06-07T03:01:32Z A nanotube phenotype where a cell or cells lack the ability to produce nanotubes. OMP:0000247 mchibucos microbial_phenotype A nanotube phenotype where a cell or cells lack the ability to produce nanotubes. OMP:JCH biofilm architecture phenotype 2011-06-07T03:05:56Z A biofilm phenotype dealing with the structural formation of the biofilm. OMP:0000248 mchibucos microbial_phenotype A biofilm phenotype dealing with the structural formation of the biofilm. OMP:WAM decreased hemolysis 2011-06-07T03:19:25Z An altered hemolysis phenotype where hemolysis is decreased relative to a designated control. OMP:0000249 mchibucos microbial_phenotype An altered hemolysis phenotype where hemolysis is decreased relative to a designated control. OMP:WAM altered cell division 2020-07-22T22:55:26Z A cellular process phenotype observed in the vegetative growth phase of the life cycle in which cell division is altered relative to a designated control. OMP:0000250 abnormal cell division microbial_phenotype siegele A cellular process phenotype observed in the vegetative growth phase of the life cycle in which cell division is altered relative to a designated control. OMP:das FYPO:0000186 abnormal cell division altered cell division ratio variability 2020-07-22T22:58:18Z OMP:0000251 microbial_phenotype siegele metabolite accumulation 2011-07-21T12:51:15Z A metabolic phenotype that deals with the accumulation of small intermediate or products of metabolism. OMP:0000252 mchibucos microbial_phenotype A metabolic phenotype that deals with the accumulation of small intermediate or products of metabolism. OMP:JCH gene expression phenotype 2011-07-21T01:03:06Z A microbial phenotype that affects expression of a gene or genes. Gene expression includes transcription, RNA processing, and, for protein-coding genes, translation and protein maturation. FYPO:0000142 GO:0010467 OMP:0000253 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A microbial phenotype that affects expression of a gene or genes. Gene expression includes transcription, RNA processing, and, for protein-coding genes, translation and protein maturation. ISBN:9781615835409 OMP:WAM gene expression GO:0010467 gene expression phenotype FYPO:0000142 constitutive transcription 2011-07-21T01:05:42Z An increased transcription phenotype where a gene or genes whose transcription is normally regulated are now transcribed constitutively. OMP:0000254 constitutive gene expression mchibucos microbial_phenotype An increased transcription phenotype where a gene or genes whose transcription is normally regulated are now transcribed constitutively. OMP:WAM plating morphology phenotype 2011-07-21T01:34:48Z A growth phenotype related to the morphology of colonies on solid medium. OMP:0000255 This term was made obsolete because it is redundant with OMP:0000100 ! colony morphology phenotype. mchibucos microbial_phenotype true A growth phenotype related to the morphology of colonies on solid medium. OMP:WAM MacConkey agar phenotype 2011-07-21T01:35:25Z A colony morphology phenotype that describes the appearance of colonies on MacConkey agar indicator medium. ** This term was made obsolete because the appearance of colonies on MacConkey agar was determined to be evidence for a phenotype rather than a phenotype itself. OMP:0000256 This term was made obsolete because the appearance of colonies on MacConkey agar was determined to be evidence for a phenotype rather than a phenotype itself. mchibucos microbial_phenotype true A colony morphology phenotype that describes the appearance of colonies on MacConkey agar indicator medium. ** This term was made obsolete because the appearance of colonies on MacConkey agar was determined to be evidence for a phenotype rather than a phenotype itself. OMP:AZ decreased cell division ratio variability 2020-07-22T23:00:48Z OMP:0000257 microbial_phenotype siegele red colony on MacConkey agar 2011-07-21T01:38:10Z A colony morphology phenotype where cells form a red colony on MacConkey agar medium. OMP:0000258 This term was made obsolete because 'red colony on MacConkey agar' was determined to be evidence for a phenotype, i.e. utilization of a particular sugar, rather than the phenotype itself. mchibucos microbial_phenotype true A colony morphology phenotype where cells form a red colony on MacConkey agar medium. OMP:AZ increased cell division ratio variability 2020-07-22T23:00:48Z OMP:0000259 microbial_phenotype siegele altered nucleoid area 2020-07-22T23:02:57Z OMP:0000260 microbial_phenotype siegele decreased nucleoid area 2020-07-22T23:04:02Z OMP:0000261 microbial_phenotype siegele increased nucleoid area 2020-07-22T23:04:02Z OMP:0000262 microbial_phenotype siegele altered nucleoid area variability 2020-07-22T23:05:16Z OMP:0000263 microbial_phenotype siegele decreased nucleoid area variability 2020-07-22T23:06:26Z OMP:0000264 microbial_phenotype siegele increased nucleoid area variability 2020-07-22T23:06:26Z OMP:0000265 microbial_phenotype siegele altered cell population growth rate 2020-07-22T23:15:57Z OMP:0000266 microbial_phenotype siegele increased gene expression 2011-07-21T02:01:35Z An altered gene expression phenotype where expression of a gene or genes is increased relative to a designated control. OMP:0000267 mchibucos microbial_phenotype An altered gene expression phenotype where expression of a gene or genes is increased relative to a designated control. OMP:WAM decreased gene expression 2011-07-21T02:02:26Z An altered gene expression phenotype where expression of a gene or genes is decreased relative to a designated control. OMP:0000268 mchibucos microbial_phenotype An altered gene expression phenotype where expression of a gene or genes is decreased relative to a designated control. OMP:WAM protein activity phenotype 2011-07-21T02:05:51Z A microbial phenotype related to the enzymatic or other activity of a protein. OMP:0000269 This term was created to organize terms beneath it in the ontology. We recommend that it not be used for annotation unless an appropriate child term cannot be found or requested. During OMP call on 2016-01-27 we decided to delete the term OMP:0000269 ! protein activity phenotype because when observing a phenotype we don't know what kind of molecule is doing something, just that a particular activity is absent, present, or altered. mchibucos microbial_phenotype true A microbial phenotype related to the enzymatic or other activity of a protein. APO:0000022 OMP:WAM decreased cell population growth rate 2020-07-22T23:16:35Z OMP:0000270 microbial_phenotype siegele increased cell population growth rate 2020-07-22T23:16:35Z OMP:0000271 microbial_phenotype siegele cell morphology variability 2020-07-23T10:45:45Z OMP:0000272 microbial_phenotype siegele altered cell perimeter length 2020-07-23T11:13:40Z OMP:0000273 microbial_phenotype siegele antimicrobial agent resistance phenotype 2011-07-21T02:21:21Z A microbial phenotype related to the resistance or sensitivity of a microbe to antimicrobial agents that kill (microbiocidal) or inhibit growth (microbiostatic) of a microbe. CHEBI:33281 OMP:0000274 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. antibiotic resistance phenotype antibiotic sensitivity phenotype antifungal resistance phenotype antimetabolite resistance phenotype antimicrobial compound sensitivity phenotype antiviral resistance phenotype mchibucos microbial_phenotype antimicrobial agent CHEBI:33281 A microbial phenotype related to the resistance or sensitivity of a microbe to antimicrobial agents that kill (microbiocidal) or inhibit growth (microbiostatic) of a microbe. CHEBI:33281 OMP:MCC decreased cell perimeter 2020-07-23T11:14:11Z OMP:0000275 microbial_phenotype siegele increased cell perimeter 2020-07-23T11:14:11Z OMP:0000276 microbial_phenotype siegele altered cell perimeter length variability 2020-07-23T11:14:34Z OMP:0000277 microbial_phenotype siegele decreased cell perimeter length variability 2020-07-23T11:15:25Z OMP:0000278 microbial_phenotype siegele increased cell perimeter length variability 2020-07-23T11:15:25Z OMP:0000279 microbial_phenotype siegele increased cell length 2011-07-21T02:37:15Z An altered cell morphology in which microbial cells are longer than a designated control; i.e. the maximum distance between the cell ends is greater than a designated control. FYPO:0000017 OMP:0000280 The mukB mutant appear to have elongated cell length. This is different from cell filamentation. PMID:1989883. mchibucos microbial_phenotype elongated cell FYPO:0000017 An altered cell morphology in which microbial cells are longer than a designated control; i.e. the maximum distance between the cell ends is greater than a designated control. OMP:DAS altered cell population phenotype 2020-07-23T11:38:45Z OMP:0000281 microbial_phenotype siegele decreased population growth rate 2011-07-21T02:43:01Z An altered population growth rate phenotype where the rate at which a microbial population multiplies is decreased relative to a designated control. OMP:0000282 decreased growth rate increased doubling time increased generation time mchibucos microbial_phenotype An altered population growth rate phenotype where the rate at which a microbial population multiplies is decreased relative to a designated control. OMP:DAS increased population growth rate 2011-07-21T02:43:22Z An altered growth rate phenotype where the rate at which a microbial population multiplies is increased relative to a designated control. OMP:0000283 decreased doubling time decreased generation time increased growth rate mchibucos microbial_phenotype An altered growth rate phenotype where the rate at which a microbial population multiplies is increased relative to a designated control. OMP:DAS altered cell population growth yield 2020-07-23T12:28:35Z OMP:0000284 microbial_phenotype siegele decreased cell population growth yield 2020-07-23T12:29:32Z OMP:0000285 microbial_phenotype siegele increased cell population growth yield 2020-07-23T12:29:32Z OMP:0000286 microbial_phenotype siegele altered fraction of non-constricted cells 2020-07-23T12:46:03Z OMP:0000287 microbial_phenotype population growth phenotype siegele decreased fraction of non-constricted cells 2020-07-23T12:47:02Z OMP:0000288 microbial_phenotype siegele increased number of anucleoid cells 2011-07-21T04:07:44Z An anucleoid phenotype where the fraction of anucleoid cells in a population is increased relative to a designated control. In Escherichia coli mutations in the muk or par genes result in an increased number of anucleoid cells. OMP:0000289 mchibucos microbial_phenotype An anucleoid phenotype where the fraction of anucleoid cells in a population is increased relative to a designated control. OMP:DAS genetic material phenotype 2011-07-21T04:24:02Z A microbial phenotype dealing with the various aspects of the nucleic acid carrier of a microbe's primary genetic information. OMP:0000290 RNA This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. double stranded DNA mchibucos microbial_phenotype single stranded DNA ISBN:9780198529170 RNA A microbial phenotype dealing with the various aspects of the nucleic acid carrier of a microbe's primary genetic information. ISBN:9780198529170 OMP:WAM ISBN:9780198529170 double stranded DNA ISBN:9780198529170 single stranded DNA genophore phenotype 2011-07-21T04:25:09Z A genophore is the chromosome equivalent in any organism, cellular organelle, or virus, however, the term is commonly used to refer to chromosomes other than the nuclear chromosomes of eukaryotes. OMP:0000291 This term was obsoleted because it is rarely used. Instead, genophore phenotype is listed as a synonym of nucleoid phenotype. mchibucos microbial_phenotype true A genophore is the chromosome equivalent in any organism, cellular organelle, or virus, however, the term is commonly used to refer to chromosomes other than the nuclear chromosomes of eukaryotes. ISBN:9780195307610 ISBN:9781613441138 OMP:DAS increased fraction of non-constricted cells 2020-07-23T12:47:02Z OMP:0000292 microbial_phenotype siegele altered fraction of cells with one nucleoid 2020-07-23T12:50:06Z OMP:0000293 microbial_phenotype siegele DNA supercoiling phenotype 2011-07-21T04:46:29Z A genetic material phenotype related to supercoiling of a double-stranded DNA molecule. OMP:0000294 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A genetic material phenotype related to supercoiling of a double-stranded DNA molecule. OMP:DAS presence of negative supercoiling 2011-07-21T04:47:38Z A DNA supercoiling phenotype where the DNA twists around its axis in the opposite direction from the clockwise turns of the right-handed double helix. OMP:0000295 mchibucos microbial_phenotype underwound DNA A DNA supercoiling phenotype where the DNA twists around its axis in the opposite direction from the clockwise turns of the right-handed double helix. ISBN:9781613441138 presence of positive supercoiling 2011-07-21T04:48:22Z A DNA supercoiling phenotype where the DNA twists around its axis in the same direction as the clockwise turns of the right-handed double helix. OMP:0000296 mchibucos microbial_phenotype overwound DNA A DNA supercoiling phenotype where the DNA twists around its axis in the same direction as the clockwise turns of the right-handed double helix. ISBN:9781613441138 decreased fraction of cells with one nucleoid 2020-07-23T12:50:57Z OMP:0000297 microbial_phenotype siegele increased fraction of cells with one nucleoid 2020-07-23T12:50:57Z OMP:0000298 microbial_phenotype siegele galactose-1-phosphate uridyl transferase activity 2011-07-21T05:12:43Z An enzymatic activity phenotype where galactose-1-phosphate uridyl transferase activity is present. OMP:0000299 This term was obsoleted in response to the decision to not have terms for individual enzyme activities unless those activities are commonly used for identification or classification. mchibucos microbial_phenotype true altered fraction of cells with two nucleoids 2020-07-23T12:52:56Z OMP:0000300 microbial_phenotype siegele decreased fraction of cells with two nucleoids 2020-07-23T12:53:45Z OMP:0000301 microbial_phenotype siegele increased fraction of cells with two nucleoids 2020-07-23T12:53:45Z OMP:0000302 microbial_phenotype siegele altered correlation between nucleoid and cell constriction during cell division 2020-07-23T14:15:02Z OMP:0000303 microbial_phenotype siegele increased substrate binding 2011-07-21T05:18:58Z A substrate binding phenotype where a protein has increased affinity for a substrate. OMP:0000304 This term was obsoleted in response to the decision that Kd measurements are too granular a phenotype for OMP, at least at this time. The issue can be reconsidered if a need for such terms arises in the future. mchibucos microbial_phenotype true decreased correlation between nucleoid and cell constriction during cell division 2020-07-23T14:16:06Z OMP:0000305 microbial_phenotype siegele macromolecular biosynthesis phenotype 2011-07-21T05:44:45Z A biosynthesis phenotype dealing with the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. OMP:0000306 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A biosynthesis phenotype dealing with the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0009059 OMP:WAM DNA replication phenotype 2011-07-21T05:45:47Z A genetic material phenotype related to the process of DNA-dependent DNA replication that takes place as part of the cell cycle. GO:0044786 OMP:0000307 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype cell cycle DNA replication GO:0044786 A genetic material phenotype related to the process of DNA-dependent DNA replication that takes place as part of the cell cycle. OMP:WAM over-initiation of DNA replication 2011-07-21T05:46:05Z A DNA replication phenotype where the frequency of initiating new rounds of DNA replication is increased relative to a designated control. OMP:0000308 mchibucos microbial_phenotype A DNA replication phenotype where the frequency of initiating new rounds of DNA replication is increased relative to a designated control. OMP:WAM biosynthetic phenotype 2011-07-21T05:47:06Z A metabolic phenotype dealing with the chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. Biosynthesis OMP:0000309 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A metabolic phenotype dealing with the chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GO:0009058 small molecule biosynthesis phenotype 2011-07-21T05:49:51Z A biosynthetic phenotype dealing with the chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. OMP:0000310 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A biosynthetic phenotype dealing with the chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. OMP:JCH amino acid biosynthesis phenotype 2011-07-21T05:50:25Z A small molecule biosynthesis phenotype dealing with the metabolic pathways that take precursor molecules and synthesize amino acids by remodeling the carbon skeleton and adding an amino group or sulfur. OMP:0000311 mchibucos microbial_phenotype A small molecule biosynthesis phenotype dealing with the metabolic pathways that take precursor molecules and synthesize amino acids by remodeling the carbon skeleton and adding an amino group or sulfur. OMP:JCH locomotion phenotype 2012-04-05T11:43:53Z A microbial phenotype where the trait in question is the self-propelled movement of a microbe from one location to another. GO:0040011 OMP:0000312 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. mchibucos microbial_phenotype A microbial phenotype where the trait in question is the self-propelled movement of a microbe from one location to another. GO:0040011 OMP:MCC locomotion GO:0040011 increased correlation between nucleoid and cell constriction during cell division 2020-07-23T14:16:06Z OMP:0000313 microbial_phenotype siegele altered degree of nucleoid constriction at the onset of cell constriction 2020-07-23T14:18:50Z OMP:0000314 This is a population average. microbial_phenotype siegele decreased degree of nucleoid constriction at the onset of cell constriction 2020-07-23T14:19:22Z OMP:0000315 microbial_phenotype siegele increased degree of nucleoid constriction at the onset of cell constriction 2020-07-23T14:19:22Z OMP:0000316 microbial_phenotype siegele cell diameter phenotype 2020-11-18T10:05:19Z OMP:0000317 microbial_phenotype siegele presence of cell length variability 2020-07-26T17:23:35Z OMP:0000318 microbial_phenotype siegele cell area phenotype 2020-11-26T13:14:47Z OMP:0000319 microbial_phenotype siegele presence of cell diameter variability 2020-07-26T17:25:52Z OMP:0000320 microbial_phenotype siegele macrolide resistance phenotype 2012-11-02T01:51:04Z An antimicrobial compound resistance phenotype related to resistance or sensitivity to compounds with a macrolide ring--a large lactone ring with multiple keto and hydroxyl groups--that is linked to one or more sugars and that have antimicrobial properties. CHEBI:25105 FK506 OMP:0000321 This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. amphotericin B resistance phenotype azithromycin resistance phenotype bafilomycin A1 resistance phenotype brasilinolide A resistance phenotype brefeldin A resistance phenotype carvomycin A resistance phenotype clarithromycin resistance phenotype dirithromycin resistance phenotype erythromycin resistance phenotype josamycin resistance phenotype latrunculin B resistance phenotype macrolide sensitivity phenotype mchibucos microbial_phenotype polyketide resistance phenotype rapamycin resistance phenotype roxithromycin resistance phenotype spiramycin resistance phenotype telithromycin resistance phenotype troleandomycin resistance phenotype CHEBI:26188 polyketide resistance phenotype CHEBI:2682 amphotericin B resistance phenotype CHEBi:3732 clarithromycin resistance phenotype CHEBI:48080 brefeldin A resistance phenotype CHEBI:2955 azithromycin resistance phenotype CHEBI:49703 latrunculin B resistance phenotype An antimicrobial compound resistance phenotype related to resistance or sensitivity to compounds with a macrolide ring--a large lactone ring with multiple keto and hydroxyl groups--that is linked to one or more sugars and that have antimicrobial properties. CHEBI:25106 OMP:MCC CHEBI:9168 rapamycin resistance phenotype CHEBI:474014 dirithromycin resistance phenotype CHEBI:65514 brasilinolide A resistance phenotype CHEBI:48844 roxithromycin resistance phenotype CHEBI:31739 josamycin resistance phenotype