If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant has participant contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains contains A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. has ligand dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true true x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. in taxon w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y develops from inverse of develops from develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of true true x actively participates in y if and only if x participates in y and x realizes some active role actively participates in x has participant y if and only if x realizes some active role that inheres in y obsolete has active participant true Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. ExO:0000000 has exposure stressor Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to x has developmental contribution from y iff x has some part z such that z develops from y has developmental contribution from inverse of has developmental contribution from developmentally contributes to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within Inverse of developmentally preceded by developmentally succeeded by cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. Austin Meier Chris Mungall Marie Angelique Laporte cjm 2017-06-05T17:35:04Z has exposure stimulus A relationship that holds via some environmental process evolutionarily related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of true true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of has input Chris Mungall input of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls activity directly regulates activity of directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of activity directly negatively regulates activity of directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates molecularly increases activity of activity directly positively regulates activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true true Chris Mungall is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causal relation between material entities Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant continuant An entity that has temporal parts and that happens, unfolds or develops through time. An entity that has temporal parts and that happens, unfolds or develops through time. occurrent occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) independent continuant independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) http://purl.obolibrary.org/obo/bfo/axiom/017-002 An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) http://purl.obolibrary.org/obo/bfo/axiom/083-003 An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity material entity anatomical entity organism or virus or viroid biological entity Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. electron Elektron beta beta(-) beta-particle e e(-) e- negatron electron electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC alkaline earth metals Erdalkalimetall Erdalkalimetalle alkaline earth metal alkaline-earth metal alkaline-earth metals metal alcalino-terreux metal alcalinoterreo metales alcalinoterreos metaux alcalino-terreux alkaline earth metal atom alkaline earth metals IUPAC Erdalkalimetall ChEBI Erdalkalimetalle ChEBI alkaline earth metal ChEBI alkaline-earth metal ChEBI alkaline-earth metals ChEBI metal alcalino-terreux ChEBI metal alcalinoterreo ChEBI metales alcalinoterreos ChEBI metaux alcalino-terreux ChEBI A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion Anionen aniones anions anion Anion ChEBI anion ChEBI anion IUPAC Anionen ChEBI aniones ChEBI anions IUPAC Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet molecular entity molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chemical entity chemical entity UniProt A role played by the molecular entity or part thereof within a biological context. biological function biological role biological function ChEBI A defined linked collection of atoms or a single atom within a molecular entity. group Gruppe Rest groupe grupo grupos group group IUPAC Gruppe ChEBI Rest ChEBI groupe IUPAC grupo IUPAC grupos IUPAC A salt is an assembly of cations and anions. salt Salz Salze ionic compound ionic compounds sal sales salts sel sels salt salt IUPAC Salz ChEBI Salze ChEBI ionic compound ChEBI ionic compounds ChEBI sal ChEBI sales ChEBI salts ChEBI sel ChEBI sels ChEBI A molecular entity having a net electric charge. Ion ion Ionen iones ions ion Ion ChEBI ion ChEBI ion IUPAC Ionen ChEBI iones ChEBI ions ChEBI magnesium 12Mg Magnesium Mg magnesio magnesium magnesium atom magnesium IUPAC 12Mg IUPAC Magnesium ChEBI Mg IUPAC magnesio ChEBI magnesium ChEBI nitrogen 7N N Stickstoff azote nitrogen nitrogeno nitrogen atom nitrogen IUPAC 7N IUPAC N IUPAC Stickstoff ChEBI azote IUPAC nitrogen ChEBI nitrogeno ChEBI nonmetal Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals nonmetal atom nonmetal IUPAC Nichtmetall ChEBI Nichtmetalle ChEBI no metal ChEBI no metales ChEBI non-metal ChEBI non-metaux ChEBI nonmetal ChEBI nonmetals ChEBI A particle not known to have substructure. elementary particle elementary particles fundamental particle elementary particle IUPAC elementary particles ChEBI A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom atome atomo atoms atomus element elements atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. nucleus Atomkern Kern noyau noyau atomique nuclei nucleo nucleo atomico nucleus atomi atomic nucleus nucleus IUPAC Atomkern ChEBI Kern ChEBI noyau IUPAC noyau atomique ChEBI nuclei ChEBI nucleo IUPAC nucleo atomico ChEBI nucleus atomi ChEBI Heavy nuclear particle: proton or neutron. nucleon Nukleon Nukleonen nucleons nucleon nucleon IUPAC nucleon IUPAC Nukleon ChEBI Nukleonen ChEBI nucleons ChEBI A nutrient is a food component that an organism uses to survive and grow. nutrients nutrient nutrients ChEBI Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogens group 15 elements group V elements nitrogenoideos nitrogenoides pnictogene pnictogenes pnictogen pnictogens IUPAC group 15 elements ChEBI group V elements ChEBI nitrogenoideos ChEBI nitrogenoides ChEBI pnictogene ChEBI pnictogenes ChEBI An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group elements Hauptgruppenelement Hauptgruppenelemente main group element main group element atom main group elements IUPAC Hauptgruppenelement ChEBI Hauptgruppenelemente ChEBI main group element ChEBI An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. elemental metal elemental metals metal element metal elements metals metal atom elemental metal ChEBI elemental metals ChEBI metal element ChEBI metal elements ChEBI metals ChEBI s-block element s-block elements s-block element atom s-block element ChEBI s-block elements ChEBI Any main group element atom belonging to the p-block of the periodic table. p-block element p-block elements p-block element atom p-block element ChEBI p-block elements ChEBI macronutrient Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). leptons lepton leptons ChEBI Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). baryons baryon baryons ChEBI Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion fermions fermion fermion IUPAC fermions ChEBI A particle smaller than an atom. subatomic particles subatomic particle subatomic particles ChEBI A subatomic particle known to have substructure (i.e. consisting of smaller particles). composite particles composite particle composite particles ChEBI Hadron is a subatomic particle which experiences the strong force. hadrons hadron hadrons ChEBI A nucleus or any of its constituents in any of their energy states. nuclear particle nuclear particle nuclear particle IUPAC Any molecular entity consisting of more than one atom. polyatomic entities polyatomic entity polyatomic entities ChEBI A monoatomic or polyatomic species having one or more elementary charges of the proton. Cation cation Kation Kationen cationes cations cation Cation KEGG_COMPOUND cation ChEBI cation IUPAC Kation ChEBI Kationen ChEBI cationes ChEBI cations ChEBI A molecular entity consisting of two or more chemical elements. chemical compound heteroatomic molecular entities heteroatomic molecular entity chemical compound ChEBI heteroatomic molecular entities ChEBI A role is particular behaviour which a material entity may exhibit. role physiological role Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. dietary component dietary components food components food component dietary component ChEBI dietary components ChEBI food components ChEBI molecular process molecular_function catalytic activity receptor activity 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. biological process physiological process single organism process single-organism process 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. GOC:go_curators GOC:isa_complete true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups all root all all Cercidospora exigua Didymosphaeria exigua Didymella exigua Cercidospora exigua Didymosphaeria exigua Trematosphaeria Botryosphaeria quercus Botryosphaeria quercuum Botryosphaeria quercus Amphobotrys Botrytis ricini Amphobotrys ricini Botrytis ricini Viscaceae Psittacantheae Lorantheae Psittacanthinae Loranthinae Kluyveromyces marxianus DMKU3-1042 Benincaseae Cucurbiteae Sweet potato leaf curl virus Hericium laciniatum Hericium ramosum Hericium coralloides Hericium laciniatum Hericium ramosum Verticillium dahliae var. longisporum Verticillium longisporum Verticillium dahliae var. longisporum Aphanomyces Aphanomyces euteiches true European wheat mosaic virus soil-borne rye mosaic virus Soil-borne cereal mosaic virus European wheat mosaic virus soil-borne rye mosaic virus Choanephora infundibulifera f. cucurbitarum Choanephora cucurbitarum Choanephora infundibulifera f. cucurbitarum Gilbertellaceae Choanephoraceae Gilbertellaceae Gilbertella Gilbertella persicaria Cochliobolus miyabeanus Drechslera oryzae Helminthosporium oryzae Luttrellia oryzae Bipolaris oryzae Cochliobolus miyabeanus Drechslera oryzae Helminthosporium oryzae Luttrellia oryzae Monographella nivalis Phyllachora graminis Pezicula Ganoderma tornatum Ganoderma zonatum Peronospora viciae Anomiidae Anomia Vira Viridae viruses Viruses Vira Viridae viruses Asteroideae Astereae Anthemideae Senecioneae Helenieae Heliantheae Mutisieae Cardueae Glomerellales Australiascaceae Ceratocystidaceae Actinomyces ipomoea Streptomyces ipomoea Streptomyces ipomoeae Actinomyces ipomoea Streptomyces ipomoea Stereaceae Peniophoraceae Plectosphaerellaceae Ashbya gossypii FDAG1 Eremothecium gossypii FDAG1 Ashbya gossypii FDAG1 Puccinia aff. coronata ML-2011 Verticillium Verticillium <family Plectosphaerellaceae> Verticillium Bursaphelenchus sp. st1_10 Aphelenchoides sp. st1_30 Paratrichodorus sp. st5_29 Trichodorus sp. st7_13 Exobasidium sp. agrFF416 Physalospora sp. agrFF592 Zizania palustris Chaetosphaeriaceae anamorphic Bionectriaceae Bionectriaceae anamorphic Bionectriaceae Pseudomonas fluorescens str. Q2-87 Pseudomonas fluorescens strain Q2-87 Pseudomonas fluorescens Q2-87 Pseudomonas fluorescens str. Q2-87 Pseudomonas fluorescens strain Q2-87 Aureobasidium pullulans var. pullulans EXF-150 Aureobasidium pullulans EXF-150 Aureobasidium pullulans var. pullulans EXF-150 Gloeophyllum trabeum Pleurotaceae Cerebella Epicoccum Cerebella Drepanoidea hook-tip moths Drepanidae hook-tip moths Obtectomera Erwinia tracheiphila str. PSU-1 Erwinia tracheiphila strain PSU-1 Erwinia tracheiphila PSU-1 Erwinia tracheiphila str. PSU-1 Erwinia tracheiphila strain PSU-1 Zymoseptoria Mycosphaerella graminicola Septoria tritici Zymoseptoria tritici Mycosphaerella graminicola Septoria tritici Adenoviridae Verticillium alfalfae Elettaria Pholiota aff. astragalina PBM2975 cardamom cardamon Amomum cardamomum Elettaria cardamomum cardamom cardamon Amomum cardamomum Dialonectria Cosmospora episphaeria Cucurbitaria episphaeria Fusarium episphaeria Nectria episphaeria Sphaeria episphaeria Dialonectria episphaeria Cosmospora episphaeria Cucurbitaria episphaeria Fusarium episphaeria Nectria episphaeria Sphaeria episphaeria Microcera Aviadenovirus Septocyta Septocyta ruborum Oryza sativa/Pyricularia oryzae mixed EST library Cochliobolus tuberculatus Curvularia tuberculata Cochliobolus tuberculatus Epicoccum purpurascens Phoma epicoccina Epicoccum nigrum Epicoccum purpurascens Phoma epicoccina Mucor piriformis Pectinoida Apiosporaceae Coleosporiaceae Caulimovirus CERV Carnation etched ring virus CERV CAMV cauliflower mosaic virus CaMV Cauliflower mosaic virus CAMV cauliflower mosaic virus CaMV Phoma medicaginis Ascochyta medicaginicola Phoma medicaginis Phoma sclerotioides Leptosphaeria sclerotioides Phoma sclerotioides black scurf of potato Thanatephorus praticola Thanatephorus cucumeris black scurf of potato Thanatephorus praticola Pseudomonas syringae pv. phaseolicola str. 1644R Pseudomonas syringae pv. phaseolicola strain 1644R Pseudomonas syringae pv. phaseolicola 1644R Pseudomonas savastanoi pv. phaseolicola 1644R Pseudomonas syringae pv. phaseolicola str. 1644R Pseudomonas syringae pv. phaseolicola strain 1644R Pseudomonas syringae pv. phaseolicola 1644R Ilyonectria Typhula idahoensis Phialophora malorum Cadophora malorum Phialophora malorum Oryza sativa Japonica Group x Oryza sativa Indica Group Peronosclerospora miscanthi Geminivirus Geminiviridae Geminivirus Geminivirus subgroup I Subgroup I Geminivirus Mastrevirus Geminivirus subgroup I Subgroup I Geminivirus Geminivirus subgroup II Subgroup II Geminivirus Curtovirus Geminivirus subgroup II Subgroup II Geminivirus Geminivirus subgroup III Subgroup III Geminivirus Begomovirus Geminivirus subgroup III Subgroup III Geminivirus Cassava latent virus cassava mosaic virus African cassava mosaic virus Cassava latent virus cassava mosaic virus CSMV Chloris striate mosaic virus CSMV MSV Maize streak virus MSV Potato yellow mosaic virus tobacco yellow dwarf virus TobYDV Tobacco yellow dwarf virus tobacco yellow dwarf virus TobYDV Macrophoma WDV Wheat dwarf virus WDV bean dwarf mosaic geminivirus Bean dwarf mosaic virus bean dwarf mosaic geminivirus bean golden mosaic geminivirus Bean golden mosaic virus bean golden mosaic geminivirus BCTV beet curly top virus BCTV Beet curly top virus BCTV beet curly top virus BCTV Cryptosporiopsis bull's-eye rot Cryptosporiopsis curvispora Cryptosporiopsis malicorticis Gloeosporium malicorticis Pezicula malicorticis Neofabraea malicorticis bull's-eye rot Cryptosporiopsis curvispora Cryptosporiopsis malicorticis Gloeosporium malicorticis Pezicula malicorticis Gymnosporangium globosum unclassified Emaravirus Reoviridae RAM-1 Reoviruses Orthoreovirus RAM-1 Reoviruses Phyllocoptes Phyllocoptes gracilis Nemania Sclerotium Sclerotium <ascomycetes> Sclerotium Sclerotium Sclerotium <basidiomycetes,family Typhulaceae> Sclerotium Sclerotinia sclerotiorum WM-A1 Sclerotinia trifoliorum 06CWM-G47 Penicillium aff. janthinellum P43 Aspergillus aff. fumigatus P8 Taphrina deformans CBS 356.35 Taphrina deformans PYCC 5710 Taphrina deformans CBS 356.35 plant reovirus 1 Phytoreovirus plant reovirus 1 WTV wound tumor virus, WTV Wound tumor virus WTV wound tumor virus, WTV Physodermataceae Physoderma plant reovirus 2 Fijivirus plant reovirus 2 MRDV Maize rough dwarf fijivirus Maize rough dwarf virus MRDV Maize rough dwarf fijivirus RBSDV Rice black-streaked dwarf virus rice black-streaked dwarf virus RBSDV Rice black streaked dwarf virus RBSDV Rice black-streaked dwarf virus rice black-streaked dwarf virus RBSDV RDV rice dwarf phytoreovirus rice dwarf phytoreovirus RDV rice dwarf virus RDV Rice dwarf virus RDV rice dwarf phytoreovirus rice dwarf phytoreovirus RDV rice dwarf virus RDV Plant reovirus subgroup 3 Oryzavirus Plant reovirus subgroup 3 Partitiviridae Saccharomyces cerevisiae/ Pachysolen tannophilus fusant Saccharomyces cerevisiae/Pachysolen tannophilus fusant Saccharomyces cerevisiae/ Pachysolen tannophilus fusant Helgardia acuformis Mollisia acuformis Pseudocercosporella herpotrichoides var. acuformis Ramulispora acuformis Ramulispora herpotrichoides var. acuformis Tapesia acuformis Tapesia yallundae var. acuformis Oculimacula acuformis Helgardia acuformis Mollisia acuformis Pseudocercosporella herpotrichoides var. acuformis Ramulispora acuformis Ramulispora herpotrichoides var. acuformis Tapesia acuformis Tapesia yallundae var. acuformis Thyrospora solani Stemphylium solani Thyrospora solani Enterobacter cloacae subsp. dissolvens str. SDM Enterobacter cloacae subsp. dissolvens strain SDM Enterobacter cloacae subsp. dissolvens SDM Enterobacter cloacae subsp. dissolvens str. SDM Enterobacter cloacae subsp. dissolvens strain SDM Kretzschmaria Ustulina deusta Kretzschmaria deusta Ustulina deusta Lecanicillium lecanii Torrubiella confragosa Verticillium lecanii Cordyceps confragosa Lecanicillium lecanii Torrubiella confragosa Verticillium lecanii Biscogniauxia marginata Bionectria Clonostachys Bionectria Nectriaceae Leifsonia Claviceps purpurea 20.1 Venturiales Sympoventuriaceae Phytophthora erythroseptica Sporobolomyces aff. jilinensis MCA 3774 negative-sense genome single-stranded RNA viruses Mononegavirales negative-sense genome single-stranded RNA viruses Physaridae Physaraceae Physaridae Streptomyces acidiscabies str. 84-104 Streptomyces acidiscabies strain 84-104 Streptomyces acidiscabies 84-104 Streptomyces acidiscabies str. 84-104 Streptomyces acidiscabies strain 84-104 Sphingomonas sp. alfa40b-PCA-E3-2 Peltella Achlya conspicua Aphanomyces cochlioides Curvularia trifolii Arthrinium Fungi incertae sedis Epicoccum nigrum P16 Cuscuta pentagona Celery mosaic virus ONMV Oat necrotic mottle virus ONMV Ramularia Clisosporium fragariae Coniothyrium fragariae Coniella fragariae Clisosporium fragariae Coniothyrium fragariae Elsinoe brasiliensis Sphaceloma arachidis Elsinoe arachidis Sphaceloma arachidis Macrophomina phaseolina str. MS6 Macrophomina phaseolina strain MS6 Macrophomina phaseolina MS6 Macrophomina phaseolina str. MS6 Macrophomina phaseolina strain MS6 Rhabdoviridae Aecidium sp. cui-1 Ganoderma lucidum Xiangnong No.1 Ustilago hordei Uh4857-4 Plant rhabdovirus subgroup A Cytorhabdovirus Plant rhabdovirus subgroup A Plant rhabdovirus subgroup B plant rhabdoviruses subgroup B Nucleorhabdovirus Plant rhabdovirus subgroup B plant rhabdoviruses subgroup B Aspergillaceae Thermoascaceae Cuscuta glomerata Pleurotus ostreatus PC9 Corynebacterium sp. mare20 Caryophylleae Cerrena unicolor 303 Trametes versicolor 84 Nigrospora Nigrospora sphaerica Hexagonia Hexagonia <basidiomycetes> Hexagonia Hexagonia hydnoides Tylenchidae Anguininae Mesoanguina Subanguina Mesoanguina Subanguina radicicola Anguinidae Beet mosaic virus Anomioidea Monascus purpureus NRRL 1596 Brevicellicium Odontia olivascens Brevicellicium olivascens Odontia olivascens Cercospora longissima true Pythium heterothallicum Pythium iwagamai Pythium iwayamae Pythium iwayamai Pythium iwagamai Pythium iwayamae Pythium paddicum Pythium pulchrum Meloidogyne cruciani Monascus ruber NRRL 1597 Phacidiopycnis sp. stklk7 Pichiaceae Peronospora pisi Peronospora viciae f.sp. pisi Peronospora viciae f. sp. pisi Peronospora pisi Peronospora viciae f.sp. pisi Wickerhamomycetaceae Phaffomycetaceae Wickerhamomycetaceae Claviceps virens Villosiclava virens Ustilaginoidea virens Claviceps virens Villosiclava virens unclassified Solanaceae Aspergillus glaucus CBS 516.65 INSV Impatiens necrotic spot virus INSV Impatiens necrotic spot virus INSV Impatiens necrotic spot virus INSV true Eubrachyura Brachyrhyncha Heterotremata Brachyrhyncha environmental Halophage eHP-E5 Corallomycetella Corallomyces mauritiicola Nectria mauritiicola Rhizostilbella hibisci Sphaerostilbe repens Corallomycetella repens Corallomyces mauritiicola Nectria mauritiicola Rhizostilbella hibisci Sphaerostilbe repens Ustilago segetum var. tritici Ustilago segetum var. tritici (Pers.) Brunaud, 1878 Ustilago tritici Ustilago segetum var. tritici Ustilago segetum var. tritici (Pers.) Brunaud, 1878 Fusarium moniliforme Gibberella moniliformis Fusarium verticillioides Fusarium moniliforme Gibberella moniliformis Trachysphaera Trachysphaeridae Galactomyces candidum Dipodascus geotrichum Endomyces geotrichum Galactomyces candidus Galactomyces geotrichum Oospora lactis Geotrichum candidum Galactomyces candidum Dipodascus geotrichum Endomyces geotrichum Galactomyces candidus Galactomyces geotrichum Oospora lactis Colletotrichum sublineolum Colletotrichum sublineola Colletotrichum sublineolum Cytospora true Teleostomi bony vertebrates Euteleostomi bony vertebrates Asperisporium Cercospora caricae Fusicladium caricae Pucciniopsis caricae Asperisporium caricae Cercospora caricae Fusicladium caricae Pucciniopsis caricae Burkholderia glumae str. AU6208 Burkholderia glumae strain AU6208 Burkholderia glumae AU6208 Burkholderia glumae str. AU6208 Burkholderia glumae strain AU6208 Rosoideae incertae sedis Nelson Bay virus Nelson bay reovirus Nelson Bay orthoreovirus Nelson Bay virus Nelson bay reovirus Plenodomus Puccinia graminis f. sp. tritici 87KEN3018-4 Agrobacterium biovar 1 Agrobacterium tumefaciens complex Agrobacterium biovar 1 Fragariinae Pentazonia Alternaria humuli Burkholderia group Burkholderiaceae Burkholderia group unclassified Burkholderiales Enoplea Adenophorea Chromadorea Adenophorea Luteoviridae Betaluteovirus Potleavirus luteovirus subgroup II Polerovirus Betaluteovirus Potleavirus luteovirus subgroup II mixed EST libraries mixed EST libraries <eukaryotes> mixed EST libraries Hansenula subpelliculosa Pichia subpelliculosa Wickerhamomyces subpelliculosa Wickerhamomyces subpelliculosus Hansenula subpelliculosa Pichia subpelliculosa Wickerhamomyces subpelliculosa unclassified Anulavirus Dendrophoma Sweet potato leaf curl China virus Pseudomonas marginalis ICMP 9505 CarMV Carnation mottle virus CarMV TCV Turnip crinkle virus TCV Alternaria raphani Alternaria japonica Alternaria raphani Helminthosporium tenuissimum Alternaria tenuissima Helminthosporium tenuissimum Bipolaris pedicellata Drechslera pedicellata Helminthosporium pedicellatum Setosphaeria pedicellata Trichometasphaeria pedicellata Exserohilum pedicellatum Bipolaris pedicellata Drechslera pedicellata Helminthosporium pedicellatum Setosphaeria pedicellata Trichometasphaeria pedicellata Helminthosporium vesicarium Helmisporium vesicarium Macrosporium vesicarium Pleospora alfalfae Pleospora herbarum Pleospora herbarum var. herbarum Pleospora pomorum Pleospora sedicola Pleospora tomatonis Sphaeria herbarum Stemphylium alfalfae Stemphylium brassicicola Stemphylium cremanthodii Stemphylium herbarum Stemphylium sedicola Stemphylium tomatonis Stemphylium vesicarium Helminthosporium vesicarium Helmisporium vesicarium Macrosporium vesicarium Pleospora alfalfae Pleospora herbarum Pleospora herbarum var. herbarum Pleospora pomorum Pleospora sedicola Pleospora tomatonis Sphaeria herbarum Stemphylium alfalfae Stemphylium brassicicola Stemphylium cremanthodii Stemphylium herbarum Stemphylium sedicola Stemphylium tomatonis Stemphylium sarcinaeforme Stemphylium sarciniforme Stemphylium sarcinaeforme Alternaria sect. Ulocladium Ulocladium atrum Alternaria atra Ulocladium atrum Ustilago kolleri Ustilago segetum Ustilago hordei Ustilago kolleri Ustilago segetum Phaeosphaeria avenaria f. sp. tritici 1 MM-2012 Stagonospora avenaria f. sp. tritici 1 MM-2012 Parastagonospora avenaria f. sp. tritici 1 MM-2012 Phaeosphaeria avenaria f. sp. tritici 1 MM-2012 Stagonospora avenaria f. sp. tritici 1 MM-2012 Verticillium dahliae JR2 Luteovirus subgroup I Luteovirus Luteovirus subgroup I BYDV barley yellow dwarf virus BYDV barley yellow dwarf virus, BYDV Barley yellow dwarf virus BYDV barley yellow dwarf virus BYDV barley yellow dwarf virus, BYDV BLRV Bean leaf roll virus Bean leafroll virus BLRV Bean leaf roll virus BWYV Beet western yellow virus Beet western yellows virus BWYV Beet western yellow virus PLRV Potato leaf roll virus Potato leaf-roll virus Potato leafroll virus PLRV Potato leaf roll virus Potato leaf-roll virus Albugo candida Ac 2V Soybean dwarf virus Eupulmonata Marafivirus Pleospora tarda Stemphylium botryosum Pleospora tarda Ustilago aegilopsidis Ustilago nigra Ustilago avenae Ustilago aegilopsidis Ustilago nigra Ecdysozoa Lophotrochozoa Trematosphaeriaceae Aphelenchoidea Pythiales Phaeosphaeria nodorum Sn4 Parastagonospora nodorum Sn4 Phaeosphaeria nodorum Sn4 Velvet tobacco mottle virus group Sobemovirus Velvet tobacco mottle virus group SBMV southern bean mosaic virus, SBMV Southern bean mosaic virus SBMV southern bean mosaic virus, SBMV Tombusvirus TBSV tomato bushy stunt tombusvirus TBSV Tomato bushy stunt virus TBSV tomato bushy stunt tombusvirus TBSV Fusicoccum amygdali Phomopsis amygdali Diaporthe amygdali Fusicoccum amygdali Phomopsis amygdali Tymovirus Sphacelia Glomerella cingulata f. sp. camelliae Colletotrichum gloeosporioides f. sp. camelliae Glomerella cingulata f. sp. camelliae Closterovirus BYV SBYV sugar beet yellows virus, SBYV Sugar beet yellows virus Beet yellows virus BYV SBYV sugar beet yellows virus, SBYV Sugar beet yellows virus Citrus tristeza closterovirus citrus tristeza closterovirus CTV citrus tristeza virus CTV Citrus tristeza virus Citrus tristeza closterovirus citrus tristeza closterovirus CTV citrus tristeza virus CTV Phyllosticta Guignardia endophyllicola Guignardia mangiferae Phyllosticta capitalensis Guignardia endophyllicola Guignardia mangiferae Carlavirus CLV Carnation latent virus CLV PVM Potato virus M PVM Pepino latent virus potato virus S PVS Potato virus S Pepino latent virus potato virus S PVS Shallot latent carlavirus Shallot latent virus Shallot latent carlavirus Capillovirus ACLSV Apple chlorotic leaf spot trichovirus apple chlorotic leaf spot virus ACLSV-A Apple chlorotic leaf spot virus ACLSV Apple chlorotic leaf spot trichovirus apple chlorotic leaf spot virus ACLSV-A Potexvirus CYMV Clover yellow mosaic potexvirus Clover yellow mosaic virus CYMV Clover yellow mosaic potexvirus Cymbidium mosaic potexvirus Cymbidium mosaic virus Cymbidium mosaic potexvirus PMV Papaya mosaic potexvirus Papaya mosaic virus PMV Papaya mosaic potexvirus PAMV potato aucuba mosaic potexvirus potato aucuba mosaic potexvirus PAMV potato aucuba mosaic virus PAMV Potato aucuba mosaic virus PAMV potato aucuba mosaic potexvirus potato aucuba mosaic potexvirus PAMV potato aucuba mosaic virus PAMV PVX potato virus X, PVX Potato virus X PVX potato virus X, PVX Penicillium chrysogenum KF-25 WClMV White clover mosaic virus WClMV Depazea batatas Phyllosticta batatas Phomopsis ipomoeae-batatas Depazea batatas Phyllosticta batatas Potyvirus BCMV bean common mosaic virus BCMV bean common mosaic virus, BCMV Bean common mosaic virus BCMV bean common mosaic virus BCMV bean common mosaic virus, BCMV BYMV Pea mosaic virus bean yellow mosaic potyvirus bean yellow mosaic virus BYMV bean yellow mosaic virus, BYMV pea mosaic potyvirus PMV-I Bean yellow mosaic virus BYMV Pea mosaic virus bean yellow mosaic potyvirus bean yellow mosaic virus BYMV bean yellow mosaic virus, BYMV pea mosaic potyvirus PMV-I ClYVV clover yellow vein potyvirus clover yellow vein virus CYVV Clover yellow vein virus ClYVV clover yellow vein potyvirus clover yellow vein virus CYVV CABMV Cowpea aphid-borne mosaic potyvirus adzuki bean mosaic virus cowpea Moroccan aphid-borne mosaic virus Cowpea aphid-borne mosaic virus CABMV Cowpea aphid-borne mosaic potyvirus adzuki bean mosaic virus cowpea Moroccan aphid-borne mosaic virus GarMV garlic mosaic virus, GarMV Garlic mosaic virus GarMV garlic mosaic virus, GarMV LMV Lettuce mosaic potyvirus Lettuce mosaic potyvirus (LMV) lettuce mosaic virus, LMV Lettuce mosaic virus LMV Lettuce mosaic potyvirus Lettuce mosaic potyvirus (LMV) lettuce mosaic virus, LMV PRSV Papaya ring spot virus papaya ringspot potyvirus papaya ringspot virus PRSV papaya ringspot virus, PRSV watermelon mosaic virus 1 Papaya ringspot virus PRSV Papaya ring spot virus papaya ringspot potyvirus papaya ringspot virus PRSV papaya ringspot virus, PRSV watermelon mosaic virus 1 PSbMV pea seed-borne mosaic potyvirus Pea seed-borne mosaic virus PSbMV pea seed-borne mosaic potyvirus PEMV pepper mottle virus PepMoV Pepper mottle virus PEMV pepper mottle virus PepMoV PPV Plum pox potyvirus plum pox virus PPV plum pox virus, PPV Plum pox virus PPV Plum pox potyvirus plum pox virus PPV plum pox virus, PPV PVA Potato A potyvirus potato virus A PVA potato virus A, PVA Potato virus A PVA Potato A potyvirus potato virus A PVA potato virus A, PVA Oidium sp. pm-103 SbMV soybean mosaic virus SMV soybean mosaic virus, SbMV Soybean mosaic virus SbMV soybean mosaic virus SMV soybean mosaic virus, SbMV SCMV sugarcane mosaic potyvirus sugarcane mosaic virus SCMV sugarcane mosaic virus, SCMV Sugarcane mosaic virus SCMV sugarcane mosaic potyvirus sugarcane mosaic virus SCMV sugarcane mosaic virus, SCMV TEV tobacco etch potyvirus Tobacco etch virus TEV tobacco etch potyvirus Pectobacterium TVMV tobacco vein mottling virus (TVMV) Tobacco vein mottling virus TVMV tobacco vein mottling virus (TVMV) South African passiflora virus SAPV South African passiflora virus South African passiflora virus SAPV Tobamoviridae Tobamovirus Tobamoviridae CCGMV Cucumber green mottle mosaic virus CCGMV Pythium aphanidermatum DAOM BR444 Pythium irregulare DAOM BR486 Pythium vexans DAOM BR484 Phytopythium vexans DAOM BR484 Pythium vexans DAOM BR484 Dickeya chrysanthemi NCPPB 516 Cercospora beticola ORSV Odontoglossum ringspot tobamovirus Odontoglossum ringspot virus ORSV Odontoglossum ringspot tobamovirus pepper mild mottle virus PMMV-S Pepper mild mottle virus pepper mild mottle virus PMMV-S purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives Alphaproteobacteraeota Alphaproteobacteriota proteobacteria Proteobacteria purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives Alphaproteobacteraeota Alphaproteobacteriota proteobacteria TMV tobacco mosaic virus TMV tobacco mosaic virus, TMV Tobacco mosaic virus TMV tobacco mosaic virus TMV tobacco mosaic virus, TMV Tomato mosaic virus Comovirus Andean potato mottle virus APMV Andean potato mottle virus Andean potato mottle virus APMV BPMV Bean-pod mottle virus Bean pod mottle virus BPMV Bean-pod mottle virus cowpea severe mosaic virus CPSMV Cowpea severe mosaic virus cowpea severe mosaic virus CPSMV Dianthoviridae Dianthovirus Dianthoviridae carnation ringspot virus CRSV Carnation ringspot virus carnation ringspot virus CRSV Fabavirus Nepovirus AMV nepovirus arabis mosaic virus ArMV Arabis mosaic virus AMV nepovirus arabis mosaic virus ArMV Fusarium proliferatum var. proliferatum ET1 Fusarium proliferatum ET1 Fusarium proliferatum var. proliferatum ET1 GFLV grapevine fanleaf nepovirus nepovirus grapevine fanleaf virus GFLV Grapevine fanleaf virus GFLV grapevine fanleaf nepovirus nepovirus grapevine fanleaf virus GFLV TBRV nepovirus tomato blackring virus TBRV Tomato black ring virus TBRV nepovirus tomato blackring virus TBRV TOMRSV Tomato ringspot virus TOMRSV Tobacco ringspot virus Furovirus Tobravirus Pea early browning virus pea early browning virus PEBV Pea early-browning virus Pea early browning virus pea early browning virus PEBV TRV Tobacco Rattle Tobravirus tobacco rattle virus TRV tobacco rattle virus, TRV Tobacco rattle virus TRV Tobacco Rattle Tobravirus tobacco rattle virus TRV tobacco rattle virus, TRV Hydnodontaceae Bromovirus Leucostoma leucostoma Leucostoma persoonii Valsa leucostoma Valsa persoonii Cytospora leucostoma Leucostoma leucostoma Leucostoma persoonii Valsa leucostoma Valsa persoonii Broad bean mottle virus BMV Brome mosaic virus BMV CCMV Cowpea chlorotic mottle virus CCMV Cucumovirus CMV cucumber mosaic cucumovirus cucumber mosaic cucumovirus CMV cucumber mosaic virus CMV cucumber mosaic virus, CMV Cucumber mosaic virus CMV cucumber mosaic cucumovirus cucumber mosaic cucumovirus CMV cucumber mosaic virus CMV cucumber mosaic virus, CMV Bipolaris hawaiiensis Cochliobolus hawaiiensis Pseudocochliobolus hawaiiensis Curvularia hawaiiensis Bipolaris hawaiiensis Cochliobolus hawaiiensis Pseudocochliobolus hawaiiensis peanut stunt cucumovirus peanut stunt virus PSV Peanut stunt virus peanut stunt cucumovirus peanut stunt virus PSV TAV Chrysanthemum aspermy virus tomato aspermy virus TAV-B Tomato aspermy virus TAV Chrysanthemum aspermy virus tomato aspermy virus TAV-B Ilarvirus TSV Tobacco streak virus TSV ApMV Apple mosaic virus ApMV Alfalfa mosaic virus group Alfamovirus Alfalfa mosaic virus group AMV Alfalfa mosaic virus AMV Pseudomonas oleovorans/pseudoalcaligenes group Hordeivirus BSMV barley stripe mosaic virus, BSMV Barley stripe mosaic virus BSMV barley stripe mosaic virus, BSMV Tepovirus Tenuivirus MSTV Maize stripe virus maize stripe virus MStV Maize stripe tenuivirus MSTV Maize stripe virus maize stripe virus MStV RSV Rice stripe virus rice stripe virus RSV Rice stripe tenuivirus RSV Rice stripe virus rice stripe virus RSV RHBV Rice hoja blanca virus Rice hoja blanca tenuivirus RHBV Rice hoja blanca virus unclassified bacteriophages unclassified phage unclassified phages bacterial virus bacterial viruses prokaryotic virus unclassified bacterial viruses unclassified bacteriophages unclassified phage unclassified phages bacterial virus bacterial viruses prokaryotic virus Peronospora parasitica Hyaloperonospora parasitica Peronospora parasitica Neoteleostei Eurypterygii Eurypterygia Eurypterygii Ctenosquamata Acanthomorpha Acanthomorphata Acanthomorpha Euacanthomorpha Euacanthomorphacea Euacanthomorpha Proteobacteria gamma subdivision Purple bacteria, gamma subdivision g-proteobacteria gamma proteobacteria gamma subdivision gamma subgroup Gammaproteobacteria Proteobacteria gamma subdivision Purple bacteria, gamma subdivision g-proteobacteria gamma proteobacteria gamma subdivision gamma subgroup Phyllosticta sp. zjl-1 low G+C Gram-positive bacteria low GC Gram+ Bacillaeota Bacillota Bacillus/Clostridium group Clostridium group firmicutes Firmacutes Low G+C firmicutes clostridial firmicutes firmicutes Firmicutes low G+C Gram-positive bacteria low GC Gram+ Bacillaeota Bacillota Bacillus/Clostridium group Clostridium group firmicutes Firmacutes Low G+C firmicutes clostridial firmicutes firmicutes Chalara elegans Chalara elegans Nag Raj & W.B. Kendr., 1975 Thielaviopsis basicola Torula basicola Berkeleyomyces basicola Chalara elegans Chalara elegans Nag Raj & W.B. Kendr., 1975 Thielaviopsis basicola Torula basicola Discula umbrinella Sphaeria errabunda Apiognomonia errabunda Discula umbrinella Sphaeria errabunda unassigned viruses unclassified virus unclassified viruses unassigned viruses unclassified virus Garlic virus D Garlic virus C Garlic virus B Garlic virus A Ustilaginoidea RBDV raspberry bushy dwarf virus RBDV Raspberry bushy dwarf virus RBDV raspberry bushy dwarf virus RBDV Uromyces appendiculatus SWBR1 Phakopsora pachyrhizi Thai1 BaYMV barley yellow mosaic virus, BaYMV Barley yellow mosaic virus BaYMV barley yellow mosaic virus, BaYMV barley mild mosaic virus BaMMV Barley mild mosaic virus barley mild mosaic virus BaMMV Cercospora aff. canescens CBS 153.55 Paraphaeosphaeria Paraphaeosphaeria michotii Armillaria solidipes RNA1 Armillaria ostoyae RNA1 Armillaria solidipes RNA1 Massarineae Cylindrocarpon sp. lbl4 Erwinia amylovora CFBP 1232 Ceratorhiza Alternaria solani f. sp. lycopersici CLRV Cherry leafroll virus cherry leaf roll nepovirus cherry leaf roll nepovirus CLRV Cherry leaf roll virus CLRV Cherry leafroll virus cherry leaf roll nepovirus cherry leaf roll nepovirus CLRV Puccinia striiformis f. sp. tritici 87/7 Colletotrichum gossypii Cochliobolus lunatus CX-3 Curvularia lunata CX-3 Cochliobolus lunatus CX-3 Magnaporthe grisea strain W97-11 Pyricularia grisea W97-11 Magnaporthe grisea strain W97-11 Rechingeriella eutypoides Monosporascus eutypoides Rechingeriella eutypoides Bacillus subtilis MB73/2 Curvularia aff. inaequalis HM-2012 Pyricularia oryzae KJ201 Mucor circinelloides B8987 Rhizopus stolonifer B9770 Septoria cucurbitacearum Rhizopus oryzae 99-133 RRV raspberry ringspot virus RRV Raspberry ringspot virus RRV raspberry ringspot virus RRV Phaeosphaeria sacchari Leptosphaeria sacchari Phaeosphaeria sacchari Ovulariopsis Haloviruses Dugaldia Hymenoxys Dugaldia Hymenoxys lemmonii Eutypa lata UCREL1 BRMV Bean rugose mosaic virus BRMV Coconut tinangaja viroid Peach latent mosaic viroid Phyllosticta coryli Avocado sunblotch viroid Chrysanthemum stunt viroid Botryotinia fuckeliana BcDW1 Botrytis cinerea BcDW1 Botryotinia fuckeliana BcDW1 unclassified unclassified. unclassified sequences unclassified unclassified unclassified. Hemileia vastatrix HvCat Acidivorax Acidovorax Acidivorax Pseudomonas cannabina pv. alisalensis str. PSa1-3 Glomerella tucumanensis Physalospora tucumanensis Colletotrichum falcatum Glomerella tucumanensis Physalospora tucumanensis Chalaropsis Polystigma Cenchrinae Phytophthora arecae Phytophthora hevea Phytophthora heveae Phytophthora hevea Coniocybomycetes Coniocybales Phytophthora inflata Phytophthora katsurae Phytophthora phaseoli Ascomycota incertae sedis Xanthomonas campestris pv. oryzicola Xanthomonas oryzae pv. oryzicola Xanthomonas campestris pv. oryzicola Becurtovirus Chalara Flammulina velutipes L11 Ceratocystis paradoxa Ceratostomella paradoxa Chalara paradoxa Endoconidiophora paradoxa Ophiostoma paradoxum Sporoschisma paradoxum Thielaviopsis paradoxa Ceratocystis paradoxa Ceratostomella paradoxa Chalara paradoxa Endoconidiophora paradoxa Ophiostoma paradoxum Sporoschisma paradoxum Pyrenophora semeniperda CCB06 Pyrenophora seminiperda CCB06 Pyrenophora semeniperda CCB06 Sphaerella pomi Mycosphaerella pomi Sphaerella pomi Phomopsis ganjae Diaporthe ganjae Phomopsis ganjae Fuchsia Anserineae Chenopodioideae charophyte/embryophyte group Charophyta/Embryophyta group Streptophytina charophyte/embryophyte group Charophyta/Embryophyta group Cherry mottle leaf virus Mycovelosiella Mycovellosiella Mycovelosiella Passalora Phaeoisariopsis Phaeoisariopsis griseola Phaeoramularia Pseudocercospora Stigmina Stigmina <ascomycetes> Stigmina Schizophyllum commune Loenen D Exobasidium vaccinii MPITM Zopfia rhizophila CBS 207.26 Laetiporus sulphureus 93-53 biota cellular organisms biota biota Armillaria mellea 131 Phytophthora parasitica P1976 Fusarium culmorum CS7071 Acrocalymma Pholiota Cercospora canescens Cercospora apii Rhizoctonia Myrothecium sp. cp0024d Fusarium sp. FSSC_8a KOD-2010 Neocosmospora vasinfecta Neocosmospora vasinfecta var. vasinfecta Fusarium neocosmosporiellum Fusarium sp. FSSC_8a KOD-2010 Neocosmospora vasinfecta Neocosmospora vasinfecta var. vasinfecta Lentinus tigrinus ALCF2SS1-6 Rathayibacter tritici NCPPB 1857 Rathayibacter iranicus VKM Ac-1602 = NCPPB 2253 Rathayibacter iranicus NCPPB 2253 Rathayibacter iranicus VKM Ac-1602 Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602 Rathayibacter iranicus VKM Ac-1602 = NCPPB 2253 Rathayibacter iranicus NCPPB 2253 Rathayibacter iranicus VKM Ac-1602 Tilletia Fusarium lateritium species complex stinking smut of wheat wheat bunt fungus Tilletia tritici Tilletia caries stinking smut of wheat wheat bunt fungus Tilletia tritici Tilletia contraversa dwarf bunt fungus Tilletia controversa Tilletia contraversa dwarf bunt fungus Fusarium decemcellulare species complex split-tongued squamates Bifurcata split-tongued squamates Lelliottia Heterodera hordecalis Candida albicans CEC2023 Euphorbia subg. Chamaesyce Raf., 1817 Chamaesyce Euphorbia subg. Chamaesyce Raf., 1817 Euphorbia sect. Plagianthae Euphorbia sect. Poinsettia Euphorbia subsect. Stormieae Cercospora citrullina Dipnotetrapodomorpha Carya Passiflora aff. ekmanii KEPU-2013 Dendranthema Chrysanthemum Dendranthema Alternaria saponariae Comoclathris Clerodendron Clerodendrum Clerodendron Capnodiales coffee Psilanthus Coffea coffee Psilanthus arabica coffee coffee Coffea arabica arabica coffee coffee Rhizopodaceae Gilbertelloideae Choanephoroideae Mucorineae hazelnuts Corylus hazelnuts European hazelnut Corylus avellana European hazelnut downy mildew Peronospora farinosa downy mildew Cylindrocarpon Cercospora gerberae Cercospora brassicicola Peronospora farinosa f. sp. spinaciae Parastagonospora Leptosphaeria avenaria Phaeosphaeria avenaria Septoria avenae Stagonospora avenae Parastagonospora avenae Leptosphaeria avenaria Phaeosphaeria avenaria Septoria avenae Stagonospora avenae Exacum Exacum gracilipes Exacum affine Exacum gracilipes Sphaerotheca xanthii Podosphaera xanthii Sphaerotheca xanthii Pycnoporus coccineus BRFM310 Trametes coccinea BRFM310 Pycnoporus coccineus BRFM310 Piloselloides Gerbera Piloselloides Transvaal daisy Gerbera jamesonii Transvaal daisy Glomerella Glomerella <ascomycetes> Glomerella Zygosaccharomyces bailii ISA1307 Lysobacterales Xanthomonadales Lysobacterales Heterobasidion Pseudomonadaceae Heterobasidion annosum Pseudomonas viridiflava TA043 Mucor racemosus B9645 Rhizopus microsporus B9738 Cercospora sorghi Septorella sorghi Ramulispora sorghi Cercospora sorghi Septorella sorghi Cercospora zeae-maydis Uromyces striatus corky root of lettuce Rhizomonas suberifaciens Sphingobium suberifaciens Sphingomonas suberifaciens Rhizorhapis suberifaciens corky root of lettuce Rhizomonas suberifaciens Sphingobium suberifaciens Sphingomonas suberifaciens Pseudomonas fuscovaginae ICMP 5940 Phaeocryptopus gaeumannii CBS 267.37 Nothophaeocryptopus gaeumannii CBS 267.37 Phaeocryptopus gaeumannii CBS 267.37 Leptosphaeria nodorum Phaeosphaeria nodorum Septoria nodorum Stagonospora nodorum Parastagonospora nodorum Leptosphaeria nodorum Phaeosphaeria nodorum Septoria nodorum Stagonospora nodorum Pseudomonas aeruginosa group fluorescent pseudomonads Pseudomonas fluorescens group fluorescent pseudomonads Pseudomonas syringae group Sphingomonas Vaccinium Cylindrocladiella Cylindrocladium parvum Cylindrocladiella parva Cylindrocladium parvum American cranberry large cranberry Oxycoccus macrocarpos Vaccinium macrocarpon American cranberry large cranberry Oxycoccus macrocarpos Pleospora betae Phoma betae Pleospora betae Myxogastromycetidae Pratylenchus zeae Perenniporia medulla-panis Ipomovirus Pantoea ananatis BD442 Peniophora sp. monte123 Thanatephorus cucumeris JGI SC002DCMIDF annual rape canola Brassica napus subsp. napus Brassica napus subsp. oleifera Brassica napus var. oleifera Brassica napus var. napus annual rape canola Brassica napus subsp. napus Brassica napus subsp. oleifera Brassica napus var. oleifera Seiridium Moniliophthora roreri MCA 2997 Synchytrium aureum Boletus supinus Fomes supinus Fomitopsis supina Polyporus supinus Scindalma supinum Fomitella supina Boletus supinus Fomes supinus Fomitopsis supina Polyporus supinus Scindalma supinum Bacillus/Staphylococcus group Bacillales Bacillus/Staphylococcus group Bacillus Bacillus rRNA group 1 Bacillus <firmicutes> Bacillus Bacillus rRNA group 1 Cylindrosporium pistaciae Phloeospora pistaciae Septoria pistaciae Cylindrosporium pistaciae Phloeospora pistaciae Septoria pistaciarum Cocos coconut palm Cocos nucifera coconut palm Potato latent virus Agaricomycotina incertae sedis Hypochnicium Hyphodontia aspera Citrus sp. kk53 Boletus populinus Rigidoporus populinus Oxyporus populinus Boletus populinus Rigidoporus populinus Hymenochaete Hymenochaetales Physisporinus Colletotrichum graminicola iJAB2 Burkholderia cepacia JBK9 Botrytis aclada Botrytis squamosa Botrytis squamosa J.C.Walker Botryotinia squamosa Botrytis squamosa Botrytis squamosa J.C.Walker Botrytis byssoidea Dictyochaeta Dictyochaeta fertilis Enterobacter cloacae UCI 29 Helminthosporium solani B-AC-16A Pythium aristosporum Pythium tracheiphilum Neonectria Haematonectria haematococca Nectria haematococca Nectria haematococca var. brevicona Neocosmospora haematococca [Nectria] haematococca Haematonectria haematococca Nectria haematococca Nectria haematococca var. brevicona Neocosmospora haematococca Eutypella pie cherry sour cherry Cerasus vulgaris Prunus cerasus pie cherry sour cherry Cerasus vulgaris Bacillus fructosus Bacillus megaterium Bacillus fructosus Trametes sp. zzu1 Pleurotus sp. ql-11 Coprinus sp. ql-8 Allexivirus Penicillium expansum T01 Cercospora caribaea Phaeoramularia manihotis Cercospora caribaea Pichia aff. alni PLE2W3 Puccinia horiana BY2013C01 Bacillus mesentericus Bacillus natto Bacillus subtilis/Bacillus globigii Bacillus uniflagellatus Vibrio subtilis Bacillus subtilis Bacillus mesentericus Bacillus natto Bacillus subtilis/Bacillus globigii Bacillus uniflagellatus Vibrio subtilis Burkholderia andropogonis Ba3549 Paraburkholderia andropogonis Ba3549 Robbsia andropogonis Ba3549 Burkholderia andropogonis Ba3549 Paraburkholderia andropogonis Ba3549 Curvularia carica-papayae Curvularia caricae-papayae Curvularia carica-papayae Phyllostictaceae Macrodiplodiopsis Gloeosporium castaneicola Gloeosporium castanicola Pilidiella castaneicola Coniella castaneicola Gloeosporium castaneicola Gloeosporium castanicola Pilidiella castaneicola Dickeya dadantii DCE-01 Eumycetozoa Zopf, 1884 Mycetozoa mycetozoans Eumycetozoa Eumycetozoa Zopf, 1884 Mycetozoa mycetozoans Ascochyta sorghi Aspergillus flavus FRR 4351 Sclerotinia borealis F-4128 Cercospora arachidicola Mycosphaerella arachidis Cercospora arachidicola Plasmopara viticola Pseudoperonospora Pseudoperonospora cubensis Trichoderma harzianum T23 Erwinia sp. ho35 Acrogymnospermae Mesangiospermae Petrosaviidae Pentapetalae Benyvirus Neofabraea perennial canker of apple Cryptosporiopsis perennans Pezicula perennans Neofabraea perennans perennial canker of apple Cryptosporiopsis perennans Pezicula perennans Pseudomonas cichorii JBC1 Rhodococcus fascians A3b Cercospora palmivora Exosporium palmivorum Sciniatosporium palmivorum Stigmina palmivora Cercospora palmivora Exosporium palmivorum Sciniatosporium palmivorum Pseudoepicoccum Epicoccum cocos Pseudoepicoccum cocos Epicoccum cocos Pinales Pseudomonas aeruginosa BWH033 Globisporangium Corynespora cassiicola Philippines Fusarium graminearum CS3005 Aspergillus niger NRRL3 Bacillus megaterium Q3 Xylella fastidiosa J1a12 Pseudomonas pseudoalcaligenes AD6 Bipolaris spicifera Brachycladium spiciferum Cochliobolus spicifer Dendryphion spiciferum Drechslera spicifera Helminthosporium spiciferum Curvularia spicifera Bipolaris spicifera Brachycladium spiciferum Cochliobolus spicifer Dendryphion spiciferum Drechslera spicifera Helminthosporium spiciferum Agrobacterium tumefaciens S2 Bulimuloidea Orthalicoidea Bulimuloidea biennial turnip rape Brassica campestris Brassica rapa (Campestris Group) Brassica rapa (Oleifera Group) Brassica rapa Winter Turnip Rape Group Brassica rapa subsp. campestris Brassica rapa subsp. silvestris Brassica rapa var. silvestris Brassica rapa var. utilis Brassica rapa subsp. oleifera biennial turnip rape Brassica campestris Brassica rapa (Campestris Group) Brassica rapa (Oleifera Group) Brassica rapa Winter Turnip Rape Group Brassica rapa subsp. campestris Brassica rapa subsp. silvestris Brassica rapa var. silvestris Brassica rapa var. utilis Ralstonia solanacearum Rs-10-244 Dorylaimia Phakopsoraceae Xanthomonas oryzae pv. oryzae PXO86 Vermicularia circinans Colletotrichum circinans Vermicularia circinans Coniothyriaceae Soja Ranunculoideae Anemoneae Cassava Ivorian bacilliform virus Acremonium sp. snG05H1 Mycena aff. murina D1.1c Bjerkandera sp. bje54 Colletotrichum sp. cse34 Ehrhartoideae Oryzoideae Ehrhartoideae Pooideae Centothecoideae Panicoideae Centothecoideae PACMAD clade Oryzeae Poeae Bromeae Triticeae Paniceae Andropogoneae Pleosporales incertae sedis true yeasts Saccharomycotina true yeasts Euascomycota Pezizomycotina Euascomycota Loculoascomycetes bitunicate ascomycetes Dothideomycetes Loculoascomycetes bitunicate ascomycetes Loculoascomycetes Plectomycetes bitunicate ascomycetes Eurotiomycetes Loculoascomycetes Plectomycetes bitunicate ascomycetes Lecanoromycetes Leotiomycetes Pezizomycetes Sordariomycetes Sordariomycetes incertae sedis Archiascomycota Taphrinomycetes Archiascomycota Pythium megalacanthum Cylindrocladiella peruviana Streptocarpinae Dothideales incertae sedis Magnaporthe grisea Pyricularia grisea Magnaporthe grisea Melanconidaceae Melanconis Apiognomonia Gnomonia Peronospora rubi Macrosporium Hendersonia Patellina Patellina <ascomycetes> Patellina Osteoglossocephalai Osteoglossocephala Euteleosteomorpha Characoidei Siluroidei Percomorphaceae Pelagimorpharia Stromateoidei Pelagiaria Pelagimorpharia Stromateoidei tunas and others Scombroidei Scombriformes tunas and others Scombroidei Carangimorpha Carangimorphariae Carangaria Carangimorpha Carangimorphariae jacks and others Carangoidei Carangiformes jacks and others Carangoidei Stiassnyiformes Ovalentaria Stiassnyiformes Cichlomorphae cichlids and convict blennies Pholidichthyiformes Cichliformes cichlids and convict blennies Pholidichthyiformes Percomorpharia Eupercaria Percomorpharia spadefishes and sicklefishes Ephippiformes spadefishes and sicklefishes Magnaporthiopsis Streptomyces sp. cr30 Botryosphaeria sp. kaf2-N2 Diaporthe sp. kaf2-Y3 Phomopsis sp. kaf1-XS(2) Pseudomonas sp. acu86 Rhizoctonia solani AG-A unclassified Phytopythium Xanthomonas sp. pist7 Fusarium solani f. sp. passiflorae Garlic virus X Acrodontium Graphiaceae Graphium Rhexographium Graphium <ascomycetes,family Graphiaceae> Graphium Rhexographium Neodevriesiaceae TAMV Tulare apple mosaic virus TAMV Paratylenchus projectus Rotylenchulus borealis Alphacryptovirus Alphapartitivirus Alphacryptovirus Benyviridae Sweet potato leaf curl Uganda virus Gymnosporangium kernianum Nicotiana tabacum/Hyoscyamus niger cybrid OSLEUM clade Monochaetia Trichosphaeriales Trichosphaeriaceae Diaporthales incertae sedis Syspastospora Syspastospora parasitica Acrostalagmus sp. ca_besc_24b Aureobasidium sp. nwa_sqmc_25_5f Drechslera sp. ca_sqma_28_3c Hypocrea sp. nc_cynh_28_3a Trichoderma sp. nc_cynh_28_3a Hypocrea sp. nc_cynh_28_3a Pyrenochaeta sp. nwa_besc_241a Ulocladium sp. nwa_sqmc_254d Candida/Lodderomyces clade Candida Candida <clade Candida/Lodderomyces clade> Candida Schizoparmaceae Crinipellis perniciosa Marasmius perniciosus Moniliophthora perniciosa Crinipellis perniciosa Marasmius perniciosus Rosa sp. cu33,10.VIII.2008 Setosphaeria turcica f. sp. sorghi [Setosphaeria] turcica f. sp. sorghi Setosphaeria turcica f. sp. sorghi Rhizoctonia leguminicola Slafractonia leguminicola Rhizoctonia leguminicola Dolichodorus heterocephalus Leptosphaeria sp. xz22 Rhizopus sp. xz12 Phoma sp. std3 Merliniidae Merliniinae Trametes pubescens Epicoccum sp. psrx-1 Rubus aff. wahlbergii MS-2014 Vararia Phytopythium MNS-2014a Phytopythium sp. MNS-2014a Phytopythium MNS-2014a Acidovorax sp. sk40 Bitylenchus brevilineatus Sauertylenchus maximus Tylenchorhynchus maximus Bitylenchus maximus Sauertylenchus maximus Tylenchorhynchus maximus rice bunt Neovossia horrida Tilletia horrida rice bunt Neovossia horrida Alternaria sp. aa11.229 Spilocaea Monosporascus Monosporascus cannonballus Tremellomycetidae Heterobasidiomycetes Tremellomycetes Tremellomycetidae Heterobasidiomycetes Agaricomycetidae sensu Kirk et al. 2001 Agaricomycetes Agaricomycetidae sensu Kirk et al. 2001 Calceolariaceae Tritimovirus environmental samples environmental samples <viruses,unclassified bacterial viruses> environmental samples Aureobasidiaceae Saccotheciei Saccotheciaceae Aureobasidiaceae Saccotheciei Pseudoidium sp. MUMH0119 Microsphaera azaleae Erysiphe azaleae Pseudoidium sp. MUMH0119 Microsphaera azaleae Microsphaera izuensis Erysiphe izuensis Microsphaera izuensis Neovossia barclayana Tilletia barclayana Neovossia barclayana Tilletia foetida Tilletia laevis Tilletia foetida Alternaria carthami Clavibacter Clavibacter xyli Leifsonia xyli Clavibacter xyli PeSV Pea streak virus PeSV OMV Oat mosaic virus OMV Heterodera ciceri Heterodera cruciferae Heterodera filipjevi Heterodera humuli Heterodera latipons Heterodera medicaginis Heterodera trifolii Punctoderinae Punctodera Punctodera punctata Deightoniella Cercospora solani Huntiella Ceratocystis moniliformis Ceratostomella moniliformis Endoconidiophora moniliformis Ophiostoma moniliforme Huntiella moniliformis Ceratocystis moniliformis Ceratostomella moniliformis Endoconidiophora moniliformis Ophiostoma moniliforme Pleosporineae incertae sedis Oncobasidium theobromae Thanatephorus theobromae Ceratobasidium theobromae Oncobasidium theobromae Thanatephorus theobromae Datronia scutellata Epidendroideae Epidendreae Laeliinae Onagroideae Circaeeae Beta vulgaris/Cercospora beticola mixed library Beta vulgaris/Cercospora beticola mixed EST library Beta vulgaris/Cercospora beticola mixed library Polyporus coccineus Pycnoporus coccineus Trametes coccinea Polyporus coccineus Pycnoporus coccineus Coriolus sanguineus Fabisporus sanguineus Microporus sanguineus Polyporus sanguineus Polystictus sanguineus Pycnoporus sanguineus Trametes sanguinea Coriolus sanguineus Fabisporus sanguineus Microporus sanguineus Polyporus sanguineus Polystictus sanguineus Pycnoporus sanguineus Phomopsis helianthi Diaporthe helianthi Phomopsis helianthi Acrocalymma medicaginis Phomopsis cucurbitae Diaporthe cucurbitae Phomopsis cucurbitae Acremonium Acremonium <Hypocreales incertae sedis> Acremonium Phloeospora Kabatiella zeae Aureobasidium zeae Kabatiella zeae wild rice Zizania wild rice Helotiales incertae sedis Fuligo Dothideomycetes incertae sedis Zopfiaceae Zopfia Zopfia rhizophila Alternaria dianthicola Saccharum aff. villosum Welker 538 true Cercospora asparagi Mucor sp. ht-7 beet Beta altissima Beta vulgaris beet Beta altissima Peronospora trifoliorum Pseudoperonospora humuli Sclerospora Protomyces graminicola Sclerospora graminicola Protomyces graminicola Plasmopara obducens Discosia Seimatosporium Hypocreales incertae sedis Microstromatales Microstromatales incertae sedis Microbotryomycetidae Microbotryomycetes Microbotryomycetidae Urediniomycetidae Pucciniomycetes Urediniomycetidae Pyricularia sp. ck2 Claviceps sp. hz-1 true Boletus sector Coriolus sector Hirschioporus sector Microporus sector Polyporus sector Polystictus sector Trichaptum sector Boletus sector Coriolus sector Hirschioporus sector Microporus sector Polyporus sector Polystictus sector Massarina walkeri Acrocalymma walkeri Massarina walkeri Cylindrocarpon ehrenbergii Cylindrocarpon magnusianum Fusarium candidum Nectria ramulariae Neonectria ramulariae Ramularia candida Neonectria candida Cylindrocarpon ehrenbergii Cylindrocarpon magnusianum Fusarium candidum Nectria ramulariae Neonectria ramulariae Ramularia candida Cicereae Dalbergieae Genisteae Phaseoleae Trifolieae Vicieae Fabeae Vicieae Coniocybaceae Ceratobasidium sp. vb-1 Hordeinae Oryzinae Saccharinae Sorghinae Tripsacinae Triticinae Zizaniinae Andropogonodae Panicodae Poodae Triticodae Rhizorhapis Corticium sasakii Hypochnus sasakii Thanatephorus sasakii Corticium sasakii Hypochnus sasakii Coryneform bacteria Corynebacteriaceae Coryneform bacteria Pantoea agglomerans group Leptosphaeria salvinii Magnaporthe salvinii Phragmoporthe salvinii Sclerotium oryzae Nakataea oryzae Leptosphaeria salvinii Magnaporthe salvinii Phragmoporthe salvinii Sclerotium oryzae Cephalotrichum Anguina Anguina tritici Ditylenchus Ditylenchus destructor Ditylenchus dipsaci Cylindrocladium sp. ecyt-2 Cladosporium cucumerinum Torulaceae Stachybotriaceae Stachybotryaceae Stachybotriaceae Helicobasidiaceae Marinoplasma Candidatus Marinoplasma Marinoplasma walnut family Juglandaceae walnut family walnuts Juglans walnuts black walnut Juglans nigra black walnut Inocutis dryophilus Inonotus dryophilus Polyporus dryophilus Inocutis dryophila Inocutis dryophilus Inonotus dryophilus Polyporus dryophilus Onnia Onnia tomentosa Phellinus ferreus Fuscoporia ferrea Phellinus ferreus Phellinus ferruginosus Fuscoporia ferruginosa Phellinus ferruginosus bleeding-heart vine glory-bower Clerodendrum thomsonae Clerodendrum thomsoniae bleeding-heart vine glory-bower Clerodendrum thomsonae Anemone coronaria wheat yellow rust Puccinia striiformis f. sp. tritici wheat yellow rust Gloeocercospora sorghi Microdochium sorghi Gloeocercospora sorghi Microdochiaceae Tachikawaea Candidatus Tachikawaea Tachikawaea Fusisporium solani Neocosmospora solani Fusarium solani Fusisporium solani Neocosmospora solani Ixoroideae Coffeeae Arecoideae Coryphoideae Cocoeae Cocoseae Cocoeae Attaleinae Phoeniceae Phakopsora Phakopsora meibomiae Physopella pachyrhizi Phakopsora pachyrhizi Physopella pachyrhizi Cercospora sp. Cladosporium sp. Phoma sp. Septoria sp. baby primrose fairy primrose Primula malacoides baby primrose fairy primrose German primrose poison primrose Primula obconica German primrose poison primrose Primula sinensis Alternaria sp. Curvularia sp. Guignardia sp. Mucor sp. Phomopsis sp. Scytalidium sp. Xylaria sp. Turicella Corynebacterium Turicella Gibberella fujikuroi complex Fusarium fujikuroi species complex Gibberella fujikuroi complex Fusarium oxysporum species complex Maloideae Spiraeoideae Amygdaloideae Maloideae Spiraeoideae Rosoideae tussock bellflower Campanula carpatica tussock bellflower Vitis sp. cv. 'Norton' Turicella sp. Corynebacterium sp. Turicella sp. true Pilidiella Coniella Pilidiella Phomopsis arctii Diaporthe arctii Phomopsis arctii Endothiella Endothiella gyrosa Aurantioideae Pestalotia adusta Pestalotiopsis adusta Pestalotia adusta Pestalotiopsis disseminata Pestalotiopsis palmarum Pestalotiopsis guepinii var. macrotricha Pestalotiopsis macrotricha Pestalotiopsis sydowiana Pestalotiopsis guepinii var. macrotricha Pestalotiopsis macrotricha Oligoplites leatherjack Oligoplites saurus leatherjack Trichiurinae Cephaleuros Cephaleuros virescens Pythium proliferatum Primula acaulis Primula vulgaris Primula acaulis Leptosphaeria sp. Coniothyrium sp. Ascochyta sp. Impatiens Impatiens subgen. Impatiens Impatiens <subgenus> Impatiens Impatiens subgen. Impatiens Fuscoporia Actinobacteria high G+C Gram-positive bacteria Actinomycetes High GC gram-positive bacteria high GC Gram+ Actinobacteria <high GC Gram+> Actinobacteria high G+C Gram-positive bacteria Actinomycetes High GC gram-positive bacteria high GC Gram+ Ramularia sp. ascomyc2 Zea mays/Colletotrichum graminicola mixed EST library Oxyporus Oxyporus <basidiomycetes> Oxyporus Ceratobasidium sp.