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ECOBASE Ontology

Contents:

Class Definitions

This section of the HTML version of the ontology contains the class definitions of the ontology. Each class defines a type of entity. A class is defined to have a set of slots, where each slot defines attributes and properties that may be used by an instance of that class.

Slots are inherited by a class from its parent classes. Usually this HTML form of the ontology shows only the names of the slots at each class, with links provided to the full definition of the slot in the slot section of the ontology. However, when the definition of a slot is changed within a class with respect to its parent, the full definition of the slot is shown.

Class: Protein-Features

Defines a region of interest on a polypeptide

Subclasses: Amino-Acid-Sites, Protein-Binding-Features, Protein-Segments

Slots:

Class: Amino-Acid-Sites

Members of this class describe modifications to, binding to,or other interesting features of one or more specific (and generally non-contiguous) amino acid residues in a polypeptide, as opposed to a larger bounded region.

Superclasses: Protein-Features

Subclasses: Selenocysteine-sites, Modified-Residues, Crosslink-Sites, Amino-Acid-Binding-Sites, Active-Sites

Slots:

Class: Selenocysteine-sites

This site contains a selenocysteine residue

Superclasses: Amino-Acid-Sites

Instances: FTR0-83, FTR0-82, FTR0-81

Slots:

Class: Modified-Residues

A site on a polypeptide in which a single residue is covalently modified

Superclasses: Amino-Acid-Sites

Subclasses: Blocking-Modifications, Formylation-Modifications, Hydroxylation-Modifications, Phosphorylation-Modifications, Sulfation-Modifications, Pyro-Glu-Modifications, Methylation-Modifications, Gamma-Carboxyglutamic-Acid-Modifications, Acetylation-Modifications, Amidation-Modifications, Glycyl-Radical-Modifications

Slots:

Class: Blocking-Modifications

Undetermined N- or C-terminal blocking group.

Superclasses: Modified-Residues

Slots:

Class: Formylation-Modifications

Formylation of the N-terminal methionine.

Superclasses: Modified-Residues

Slots:

Class: Hydroxylation-Modifications

Hydroxylation of an asparagine, aspartate, proline or lysine residue.

Superclasses: Modified-Residues

Slots:

Class: Phosphorylation-Modifications

Phosphorylation of a serine, threonine, tyrosine, aspartate or histidine residue.

Superclasses: Modified-Residues

Instances: FTR0-52, FTR0-51, FTR0-50

Slots:

Class: Sulfation-Modifications

Sulfation, generally of tyrosine

Superclasses: Modified-Residues

Slots:

Class: Pyro-Glu-Modifications

N-terminal glutamine which has formed an internal cyclic lactam to become pyrrolidone carboxylic acid.

Superclasses: Modified-Residues

Slots:

Class: Methylation-Modifications

Methylation, generally of lysine or arginine.

Superclasses: Modified-Residues

Slots:

Class: Gamma-Carboxyglutamic-Acid-Modifications

Conversion of a glutamate residue to gamma-carboxyglutamic acid.

Superclasses: Modified-Residues

Slots:

Class: Acetylation-Modifications

Acetylation, N-terminal or other.

Superclasses: Modified-Residues

Slots:

Class: Amidation-Modifications

Amidation, generally at the C-terminal of a mature active peptide.

Superclasses: Modified-Residues

Slots:

Class: Glycyl-Radical-Modifications

Superclasses: Modified-Residues

Slots:

Class: Crosslink-Sites

Superclasses: Amino-Acid-Sites

Subclasses: Interchain-Crosslinks, Intrachain-Crosslinks, Disulfide-Bond-Sites

Slots:

Class: Interchain-Crosslinks

A bond is formed between the one specified amino acid residue on this chain and an amino acid residue on another chain. The value of the ATTACHED-GROUP slot should be another instance of Interchain-Crosslinks.

Superclasses: Protein-Binding-Features, Crosslink-Sites

Subclasses: Interchain-Disulfide-Bonds

Slots:

Class: Interchain-Disulfide-Bonds

A disulfide bond is formed between the one specified cysteine residue on this chain and a cysteine residue on another chain. The value of the ATTACHED-GROUP slot should be another instance of Interchain-Disulfide-Bonds.

Superclasses: Interchain-Crosslinks, Disulfide-Bond-Sites

Slots:

Class: Intrachain-Crosslinks

The two designated residues are linked by an intrachain bond.

Superclasses: Crosslink-Sites

Subclasses: Intrachain-Disulfide-Bonds

Slots:

Class: Intrachain-Disulfide-Bonds

The two specified cysteine residues are linked to each other by a disulfide bond.

Superclasses: Disulfide-Bond-Sites, Intrachain-Crosslinks

Slots:

Class: Disulfide-Bond-Sites

A cysteine residue that forms a disulfide bond with another cysteine residue either on the same polypeptide or on a different one.

Superclasses: Crosslink-Sites

Subclasses: Intrachain-Disulfide-Bonds, Interchain-Disulfide-Bonds

Slots:

Class: Intrachain-Disulfide-Bonds

The two specified cysteine residues are linked to each other by a disulfide bond.

Superclasses: Disulfide-Bond-Sites, Intrachain-Crosslinks

Slots:

Class: Interchain-Disulfide-Bonds

A disulfide bond is formed between the one specified cysteine residue on this chain and a cysteine residue on another chain. The value of the ATTACHED-GROUP slot should be another instance of Interchain-Disulfide-Bonds.

Superclasses: Interchain-Crosslinks, Disulfide-Bond-Sites

Slots:

Class: Amino-Acid-Binding-Sites

This class describes binding (covalent or otherwise) to specific residues of a polypeptide.

Superclasses: Protein-Binding-Features, Amino-Acid-Sites

Subclasses: Metal-Binding-Sites, Lipid-Binding-Sites, Glycosylation-Sites

Slots:

Class: Metal-Binding-Sites

Binding site for a metal ion.

Superclasses: Amino-Acid-Binding-Sites

Slots:

Class: Lipid-Binding-Sites

Covalent binding of a lipid moiety

Superclasses: Amino-Acid-Binding-Sites

Slots:

Class: Glycosylation-Sites

Attachment of a glycan (mono- or polysaccharide) to this site. Linkage can be either C-, N- or O-linked.

Superclasses: Amino-Acid-Binding-Sites

Slots:

Class: Active-Sites

Amino acid(s) involved in the activity of an enzyme.

Superclasses: Amino-Acid-Sites

Slots:

Class: Protein-Binding-Features

Describes a feature that binds some other entity, such as a small molecule, site of some other protein, etc.

Superclasses: Protein-Features

Subclasses: Interchain-Crosslinks, Amino-Acid-Binding-Sites, Protein-Binding-Regions

Slots:

Class: Interchain-Crosslinks

A bond is formed between the one specified amino acid residue on this chain and an amino acid residue on another chain. The value of the ATTACHED-GROUP slot should be another instance of Interchain-Crosslinks.

Superclasses: Protein-Binding-Features, Crosslink-Sites

Subclasses: Interchain-Disulfide-Bonds

Slots:

Class: Interchain-Disulfide-Bonds

A disulfide bond is formed between the one specified cysteine residue on this chain and a cysteine residue on another chain. The value of the ATTACHED-GROUP slot should be another instance of Interchain-Disulfide-Bonds.

Superclasses: Interchain-Crosslinks, Disulfide-Bond-Sites

Slots:

Class: Amino-Acid-Binding-Sites

This class describes binding (covalent or otherwise) to specific residues of a polypeptide.

Superclasses: Protein-Binding-Features, Amino-Acid-Sites

Subclasses: Metal-Binding-Sites, Lipid-Binding-Sites, Glycosylation-Sites

Slots:

Class: Metal-Binding-Sites

Binding site for a metal ion.

Superclasses: Amino-Acid-Binding-Sites

Slots:

Class: Lipid-Binding-Sites

Covalent binding of a lipid moiety

Superclasses: Amino-Acid-Binding-Sites

Slots:

Class: Glycosylation-Sites

Attachment of a glycan (mono- or polysaccharide) to this site. Linkage can be either C-, N- or O-linked.

Superclasses: Amino-Acid-Binding-Sites

Slots:

Class: Protein-Binding-Regions

Superclasses: Protein-Binding-Features, Protein-Segments

Subclasses: Nucleotide-Phosphate-Binding-Regions, DNA-Binding-Regions, Ca-Binding-Regions

Slots:

Class: Nucleotide-Phosphate-Binding-Regions

Nucleotide-phosphate-binding region on a polypeptide

Superclasses: Protein-Binding-Regions

Slots:

Class: DNA-Binding-Regions

DNA-binding region on a polypeptide

Superclasses: Protein-Binding-Regions

Slots:

Class: Ca-Binding-Regions

Calcium-binding region on a polypeptide

Superclasses: Protein-Binding-Regions

Slots:

Class: Protein-Segments

Describes a linear region of an amino-acid chain.

Superclasses: Protein-Features, Polymer-Segments

Subclasses: Transmembrane-Regions, Zn-Finger-Regions, Signal-Sequences, Transit-Peptides, Propeptides, Chains, Active-Peptides, Repeats, Homology-Domains, Protein-Binding-Regions

Slots:

Class: Transmembrane-Regions

A feature of most intrinsic proteins of plasma or vesicular membranes; a polypeptide sequence of about seven residues if beta-sheet, up to 22 residues if alpha-helix, that connects extracellular to intracellular domains, joined by extended polypeptides on the cytoplasmic and external or vesicular sides. Receptor and ion channels have between one and twelve such domains.

Superclasses: Protein-Segments

Slots:

Class: Zn-Finger-Regions

A motif of which seven or more may appear in a DNA-binding protein. Each is characterized by two closely spaced cysteine and two histidine residues that serve as ligands for a single Zn2+. When bound to Zn2+ they form a module from which protrude amino acid side chains that interact with the bases partially exposed to the DNA major groove. Since in the area of contact there is a limited and local parallel of DNA and protein sequences, the occurrence of the contacting amino acid residues in the protein sequence falls into a regularity, or register, that creates in the protein a syllabicity.

Superclasses: Protein-Segments

Slots:

Class: Signal-Sequences

The N-terminal portion of a secretory or membrane protein that assists it across the membrane of the rough endoplasmic reticulum, where it is synthesized, but is cleaved from the protein even before the synthesis of the protein is complete. Mitochondrial and chloroplast proteins that are synthesized on ribosomes also have signal sequences that target them to their organelle; these may be N-terminal or internal, and may or may not be removed by proteolysis.

Superclasses: Protein-Segments

Slots:

Class: Transit-Peptides

In the case of post-translationally imported mitochondrial and chloroplast proteins(synthesized in the cytoplasm), an amino terminal sequence which contains targeting information and is removed during or shortly after import into the organelles.

Superclasses: Protein-Segments

Slots:

Class: Propeptides

The part of a protein that is proteolytically cleaved during the protein's maturation, e.g. the internal residues of proinsulin, the N-terminal residues of pepsinogen. The term is usually not used for a signal peptides, but for the peptides removed from protein precursors that can be isolated and that have a reasonably long half-life.

Superclasses: Protein-Segments

Slots:

Class: Chains

Extent of a polypeptide chain in a mature protein

Superclasses: Protein-Segments

Slots:

Class: Active-Peptides

Extent of a released active peptide.

Superclasses: Protein-Segments

Slots:

Class: Repeats

Extent of an internal sequence repetition

Superclasses: Protein-Segments

Slots:

Class: Homology-Domains

Describes protein regions share a high degree of sequence homology with similar regions in other proteins.

Superclasses: Protein-Segments

Slots:

Class: Protein-Binding-Regions

Superclasses: Protein-Binding-Features, Protein-Segments

Subclasses: Nucleotide-Phosphate-Binding-Regions, DNA-Binding-Regions, Ca-Binding-Regions

Slots:

Class: Nucleotide-Phosphate-Binding-Regions

Nucleotide-phosphate-binding region on a polypeptide

Superclasses: Protein-Binding-Regions

Slots:

Class: DNA-Binding-Regions

DNA-binding region on a polypeptide

Superclasses: Protein-Binding-Regions

Slots:

Class: Ca-Binding-Regions

Calcium-binding region on a polypeptide

Superclasses: Protein-Binding-Regions

Slots:


Slot Definitions

This section of the HTML version of the ontology contains the slot definitions of the ontology. Each slot itself has several properties such as documentation about that slot, a cardinality (specifying the number of values that the slot may have), a value type (specifying the data type of slot values), and a domain (specifying the class(es) in which the slot is used).

Slot NameDocumentationProperties
ABBREV-NAME This is the version of the database name that is used in links VALUE-TYPE: STRING
DOMAIN: Databases
ABSOLUTE-PLUS-1
-POS
The absolute base pair position of the promoter on the DNA strand CARDINALITY: 1
VALUE-TYPE: INTEGER
DOMAIN: Promoters
UNITS: BASE-PAIRS
QUERYABLE?: T
ABSTRACT The text of the abstract of the publication. VALUE-TYPE: STRING
DOMAIN: Publications
ACTION Encodes the type of action to be taken for a note. DOMAIN: Notes
ACTIVATORS Values of this slot are tuples containing a transcription factor and a DNA binding site. Presence of the transcription factor bound to the DNA binding site activates this RNA-Polymerase binding reaction, and therefore activates transcription. VALUE-TYPE: SEXPR
DOMAIN: Binding-Reactions
ACTIVATORS-ALL The computed set of all activators of the current enzymatic reaction, combined from all of the other activators slots. READ-ONLY: T
GET-METHODS: GET-ACTIVATORS-ALL
VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
ACTIVATORS-ALLOSTERIC Allosteric activators increase the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that increases the affinity of the enzyme to its substrates without affecting its VMAX. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
ACTIVATORS-NONALLOSTERIC Nonallosteric activators increase the specified enzyme activity by means other than allosteric. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
ACTIVATORS-UNKMECH Compounds that activate the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper(s) curated thus far do not define the mechanism, and a full literature search has yet to be performed. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
ALTERNATIVE-COFACTORS This slot records variability in the cofactors that have been observed for this enzymatic reaction. If, for example, the literature indicates that Mn+2 can substitute for Mg+2 as a cofactor in this reaction, we would list the following as a value: (Mg+2 Mn+2). VALUE-TYPE: LIST
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
ALTERNATIVE-SUBSTRATES This slot records variability in the substrates that have been observed for this enzymatic reaction. If, for example, the literature indicates that X can substitute for Y as a substrate in this reaction, we would list the following as a value: (Y X), where X and Y are the frame IDs for the corresponding substrates. VALUE-TYPE: LIST
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
ANTICODON The three bases of the tRNA, which make up the anticodon. The direction is 5' to 3' of the tRNA. This is the reverse and complementary to the sequence of the recognized codons. CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: tRNAs
APPEARS-IN-BINDING
-REACTIONS
This slot is used to cross-reference a chemical to the one or more binding reactions in which the chemical is a reactant. Binding reactions only explicitly list their reactants, but not their products, so there is no analog of this slot for products of binding reactions.

INVERSE: REACTANTS
VALUE-TYPE: Binding-Reactions
DOMAIN: Polymer-Segments, Chemicals
QUERYABLE?: T
APPEARS-IN-LEFT
-SIDE-OF
This slot lists all reactions in which this chemical appears in the left side of the reaction (as a reactant). INHERITANCE-TYPE: UNIQUE
INVERSE: LEFT
VALUE-TYPE: Reactions
DOMAIN: Chemicals
QUERYABLE?: T
APPEARS-IN-RIGHT
-SIDE-OF
This slot lists all reactions in which this chemical appears on the right side (as a product). INHERITANCE-TYPE: UNIQUE
INVERSE: RIGHT
VALUE-TYPE: Reactions
DOMAIN: Chemicals
QUERYABLE?: T
AROMATIC-RINGS Lists those atoms that participate in aromatic rings for this compound. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: LIST
DOMAIN: Compounds
HIDE-SLOT?: T
ATOM-CHARGES This slot lists the charges of specific atoms within the compound. Each value of the slot is a list of the form (A C) where A is the index of an atom in slot Structure-Atoms, and C is the charge of that atom. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: LIST
DOMAIN: Chemicals
HIDE-SLOT?: T
ATOM-CHIRALITY In analogy to the ATOM-CHARGES slot, this slot can contain multiple values, which are lists of two elements: first the atom number, and second an integer that describes the "atom stereo parity", as documented for the MDL molfile format. This parity can be 1=odd, 2=even, or 3=unspecified stereo center. The odd/even stereo parity is relative to the ordering of the atoms, as described in the MDL documentation, but not an absolute stereo designator in the sense of the CIP system. NUMERIC-MINIMUM: 0
NUMERIC-MAXIMUM: 3
INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: LIST
DOMAIN: Chemicals
HIDE-SLOT?: T
ATOMIC-NUMBER This slot stores the atomic number of a chemical element. MAXIMUM-CARDINALITY: 1
NUMERIC-MINIMUM: 1
VALUE-TYPE: NUMBER
DOMAIN: Elements
ATOMIC-WEIGHT This slot stores the atomic weight of a chemical element. MAXIMUM-CARDINALITY: 1
NUMERIC-MINIMUM: 1
VALUE-TYPE: NUMBER
DOMAIN: Elements
ATTACHED-GROUP The entity that binds to the protein feature VALUE-TYPE: (OR Chemicals Protein-Binding-Features STRING)
DOMAIN: Protein-Binding-Features
AUTHORS This slot lists the authors of a publication. Each value of this slot lists a single author. VALUE-TYPE: STRING
DOMAIN: Publications
BASAL-TRANSCRIPTION
-VALUE
A number indicating the transcription of the promoter in the absence of any regulator. VALUE-TYPE: NUMBER
DOMAIN: RNA-Polymerase-Binding-Reactions
BASE-URL Stores URL for Database home page VALUE-TYPE: STRING
DOMAIN: Databases
BASIS-FOR-ASSIGNMENT Records the basis for assignment of the protein to the reaction, whether manually by a curator (the default), or automatically by various means. VALUE-TYPE: (ONE-OF EC-NUMBER AUTOMATED-NAME-MATCH MANUAL MANUAL-AMBIGUOUS-NAME-MATCH MANUAL-NAME-TUPLE-MATCH)
DOMAIN: Enzymatic-Reactions
BOOKKEEPING-SLOT? DOMAIN: DOMAIN-SLOTS
CACHED-STATISTICS This slot is a list of the form (name1 value1 name2 value2 ....). The name-value pairs describe statistics for this object that have been precomputed and cached on this object. VALUE-TYPE: LIST
DOMAIN: Organisms, Genetic-Elements
HIDE-SLOT?: T
CANONICALIZE-FOR
-INDEX?
MAXIMUM-CARDINALITY: 1
DOMAIN: DOMAIN-SLOTS
HIDE-SLOT?: T
CATALYZES This slot points from a protein to an enzymatic-reaction frame that in turn links the protein to a reaction that the protein catalyzes. INVERSE: ENZYME
VALUE-TYPE: Enzymatic-Reactions
DOMAIN: Proteins
QUERYABLE?: T
CENTISOME-POSITION This slot lists the map position of this gene on the chromosome in centisome units. MAXIMUM-CARDINALITY: 1
NUMERIC-MINIMUM: 0
INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: NUMBER
DOMAIN: All-Genes
DIGITS-OF-PRECISION: 5
UNITS: CENTISOMES
QUERYABLE?: T
CHARGE This slot stores the net charge of a chemical, which must be an integer. MAXIMUM-CARDINALITY: 1
INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: NUMBER
DOMAIN: Compounds
QUERYABLE?: T
CHEMICAL-FORMULA Lists the empirical formula for this compound. Each value of this slot is a list of the form (ATOM COUNT) where ATOM is the ID of a frame for the corresponding element, and COUNT is the number of occurrences of that atom in this compound. For example, water would be represented as two slot values: The first value is the list (H 2). The second value is the list (O 1).

This slot applies to both small molecular weight compounds, and to proteins. In the case of proteins, it is used to encode chemical modifications to proteins, such as methylation. In this case, one of the ATOMs would be the ID of a protein frame.

INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: LIST
DOMAIN: Proteins, Chemicals
QUERYABLE?: T
CIRCULAR? When the value of this slot is TRUE it means that the genetic element is a circular as opposed to linear. CARDINALITY: 1
VALUE-TYPE: BOOLEAN
DOMAIN: Genetic-Elements
CITATIONS This slot lists general citations pertaining to the object containing the slot. Citations may or may not have evidence codes attached to them. Each value of the slot is a string of the form either "[reference-id]" or "[reference-id:evidence-code:timestamp:curator:probability]", where:

reference-id = a PubMed/Medline identifier (we prefer the PubMed id) or id for a Publication frame (w/o the leading "PUB-") evidence-code= the frame id of some subclass of |Evidence|, e.g. EV-EXP timestamp = a lisp universal time corresponding to the time the evidence code was assigned curator = the username of the curator who assigned the evidence code probability = a number between 0 and 1 describing the probability that the evidence is correct

Any of the above components may be omitted, but it is meaningless to supply a timestamp, curator or probability if the evidence-code is omitted. Trailing colons should be omitted, but if a value contains an evidence-code with no accompanying citation, the leading colon must be present. The square brackets are optional.

Examples: [123456] -- a PubMed or Medline reference [SMITH95] -- a non-PubMed reference [123456:EV-IDA] -- an evidence code with associated PubMed reference [:EV-HINF] -- an evidence code with no associated reference [123456:EV-IGI:9876543:paley] -- a time- and user-stamped evidence code with associated reference [123456:EV-AINF:9876543:paley:0.75] -- a fully instantiated evidence code and reference

INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: Polymer-Segments, Organisms, Generalized-Reactions, Enzymatic-Reactions, Chemicals
QUERYABLE?: T
CLASS-INSTANCE
-LINKS
Each value of this slot is a reaction in the pathway. Two annotations (in addition to the usual possibilities) are available on this slot: REACTANT-INSTANCES and PRODUCT-INSTANCES, whose values are compounds. If one of the reactants of the slot-value reaction is a class C and the REACTANT-INSTANCES are instances of C, then the instances are drawn as part of the pathway, with identity links to the class. The PRODUCT-INSTANCES are treated similarly. DOMAIN: Pathways
CODONS Indicates the base triplets that are recognized by the anticodon of this tRNA. The direction is 5' to 3' on the coding strand of genes. VALUE-TYPE: STRING
DOMAIN: tRNAs
COEFFICIENT pkarp: I believe this slot is no longer used in a mainstream fashion in Pathway Tools. However, Coefficient is the name of an annotation label, and in addition, it is possible that the ENZYME loader tool stores data into a slot called Coefficient. VALUE-TYPE: (OR NUMBER SYMBOL)
COFACTOR-BINDING
-COMMENT
A comment describing cofactor requirements of an enzyme. VALUE-TYPE: STRING
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
COFACTORS Cofactors are compounds that are required for an enzyme to catalyze a reaction, but that are unchanged by the reaction, and that are not tightly bound to the enzyme. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
COFACTORS-OR-PROSTHETIC
-GROUPS
Compounds that are required for an enzyme to catalyze a reaction, but that are unchanged by the reaction, and whose degree of binding to the enzyme is unknown. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
COMMENT The Comment slot stores a general comment about the object that contains the slot. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: THING
QUERYABLE?: T
COMMENT-INTERNAL A comment for internal purposes that is not released to the pubilc. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: THING
PRIVATE?: T
COMMON-NAME The primary name by which an object is known to scientists -- a widely used and familiar name (in some cases arbitrary choices must be made). MAXIMUM-CARDINALITY: 1
INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: Evidence, Polymer-Segments, Organisms, Generalized-Reactions, Enzymatic-Reactions, Chemicals, Databases
COMPARTMENT DOMAIN: NIL
COMPONENT-COEFFICIENTS This slotunit is outdated; it is kept around because it's used in templates, then altered by the template parser. NUMERIC-MINIMUM: 1
VALUE-TYPE: INTEGER
DOMAIN: Proteins
HIDE-SLOT?: T
COMPONENT-OF This slot specifies an object that contains this object as a smaller part. For example, this slot points from a monomer to a larger complex that contains it. INVERSE: COMPONENTS
VALUE-TYPE: THING
DOMAIN: Macromolecules, Polymer-Segments, Anatomical-Structures
QUERYABLE?: T
COMPONENT-POSITIONS A sorted list of the centisome positions of the componets of the chromosome. This list contains only the positions of the first N components that actually have map positions. NUMERIC-MINIMUM: 0
NUMERIC-MAXIMUM: 100
VALUE-TYPE: NUMBER
DOMAIN: Chromosomes
UNITS: CENTISOMES
COLLECTION-TYPE: LIST
COMPONENTS This slot lists the components of some physical assembly, such as the subunits of a protein complex or the genes within a chromosome. The coefficient of each component (when known) is listed as an annotation of the component value under the label coefficient.

When a modified protein is created to reflect a chemically modified alternate form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein.

INVERSE: COMPONENT-OF
VALUE-TYPE: THING
DOMAIN: Complexes, Polymer-Segments, Anatomical-Structures
QUERYABLE?: T
OPTIONAL-ANNOTATIONS: COEFFICIENT
CONTACT-EMAIL The email address of a person who serves at the primary contact for this PGDB, such as to receive questions or bug reports from users of the PGDB. CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Organisms
DATE-RESOLVED Meant to encode the date on which the issue encoded by this note was resolved. However, no code exists to implement this slot. VALUE-TYPE: INTEGER
DOMAIN: Notes
CARDINALITY-MAX: 1
DBLINKS Stores links to information about the same object in other DBs. Each value is a list of the form (DB-NAME DB-UNIQUE-ID) INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: SEXPR
DOMAIN: Polymer-Segments, Generalized-Reactions, Enzymatic-Reactions, Chemicals
DEFAULT-RECIPIENT VALUE-TYPE: People
DOMAIN: People
CARDINALITY-MAX: 1
DELTAG0 This slot contains the change in Gibbs free energy for the reaction in the direction the reaction is written. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: NUMBER
DOMAIN: Generalized-Reactions
UNITS: KCAL/MOLE
QUERYABLE?: T
DEPRESSORS Compounds or proteins known to depress or inhibit a non-enzymatic reaction. Often the mechanism is unknown -- the action may even be indirect. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Reactions
QUERYABLE?: T
DIFFICULTY VALUE-TYPE: INTEGER
DOMAIN: Notes
CARDINALITY-MAX: 1
DIGITS-OF-PRECISION The number of digits of precision that should be displayed for values of this slot on output. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: INTEGER
DOMAIN: SLOTS
DISABLE-DISPLAY When true, this slot disables display of the pathway graph for a pathway. VALUE-TYPE: BOOLEAN
DOMAIN: Pathways
HIDE-SLOT?: T
DISPLAY-COORDS
-2D
This slot lists coordinates for the display of the chemical structure of this compound in two dimensions. The values of this slot correspond one-to-one to the values of slot Structure-Atoms. Each value of this slot is of the form (X Y) and consists of the X-Y display coordinate of the corresponding atom in Structure-Atoms. The coordinates are real numbers with no specified minimum or maximum values -- they are re-scaled at display time.

INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: SEXPR
DOMAIN: Chemicals
HIDE-SLOT?: T
COLLECTION-TYPE: LIST
DNA-FOOTPRINT-SIZE For proteins that bind to DNA, the number of base pairs on the DNA strand that the binding protein covers. MAXIMUM-CARDINALITY: 1
NUMERIC-MINIMUM: 1
VALUE-TYPE: INTEGER
DOMAIN: Proteins
UNITS: BASE-PAIRS
DYNAMIC-SEARCH
-URL
Stores URL format string for dynamic searches. Format string has one arg: the search string. VALUE-TYPE: STRING
DOMAIN: Databases
EC-LIST This slot records info about retired and transfered EC numbers. VALUE-TYPE: SEXPR
DOMAIN: EC-BOOKKEEPING
EC-NUMBER The enzyme commission (EC) number of the reaction. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Reactions
QUERYABLE?: T
INHERITANCE-TYPE: UNIQUE
ENZYMATIC-REACTION Links a reaction frame to the enzymatic reaction frame(s) that connect to enzymes that catalyze this reaction. INVERSE: REACTION
VALUE-TYPE: Enzymatic-Reactions
DOMAIN: Reactions
QUERYABLE?: T
ENZYME This slot links an enzymatic reaction to the enzyme whose activity the enzymatic reaction describes. CARDINALITY: 1
MAXIMUM-CARDINALITY: 1
INVERSE: CATALYZES
VALUE-TYPE: Proteins
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
ENZYME-USE This slot allows us to specify that specific enzymes are the only enzymes that catalyze a specified reaction within the current pathway. That is, in the context of pathway P, we might want to specify that for reaction R, only two of the three known isozymes for R actually catalyze R in this pathway. This slot is used when it is specifically known that some enzymes in an organism specifically do not catalyze a given reaction in the context of some pathway, usually because of regulation.

Each value of this slot is a tuple of the form (R ER1 ... ERn) where R is a reaction frame ID, and the one or more ERi are the IDs of enzymatic reaction frames. A given tuple specifies that the enzyme linked to ER1 catalyzes R.

VALUE-TYPE: LIST
DOMAIN: Pathways
EQUILIBRIUM-CONSTANT The equilibrium constant for a reaction. VALUE-TYPE: NUMBER
DOMAIN: Reactions
QUERYABLE?: T
EVIDENCE Describes evidence for the defined function of this object. Currently we distinguish between function that is determined experimentally, and function that is determined through computational sequence analysis. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: (ONE-OF EXPERIMENT SEQUENCE-ANALYSIS)
DOMAIN: All-Genes
QUERYABLE?: T
EXTENT-UNKNOWN? The value of this slot should be T when it is not known to how many genes the transcription unit extends. CARDINALITY: 1
VALUE-TYPE: BOOLEAN
DOMAIN: Transcription-Units
FEATURE-OF Link to the polypeptide (including modified forms) to which this feature belongs INVERSE: FEATURES
VALUE-TYPE: Polypeptides
DOMAIN: Protein-Features
FEATURES Lists sites of interest (such as binding sites, modification sites, etc.) on a polypeptide. INVERSE: FEATURE-OF
VALUE-TYPE: Protein-Features
DOMAIN: Polypeptides
FIRST-NAME The first name of this person. VALUE-TYPE: STRING
DOMAIN: People
CARDINALITY-MAX: 1
FLAGGED-NOTES A list of the notes this person has seen, and has flagged for later inspection. VALUE-TYPE: Notes
DOMAIN: People
FUNCTIONAL-ASSIGNMENT
-COMMENT
Used from PathoLogic to record any research done so far or conclusions reached about matching (or not matching) the protein to a reaction. VALUE-TYPE: STRING
DOMAIN: Polypeptides
FUNCTIONAL-ASSIGNMENT
-STATUS
Describes how PathoLogic should treat a polypeptide unassigned to any reaction -- whether an enzyme or not, high-priority or not, etc. Multiple values are possible (generally in the case of a probable enzyme that is also marked as flagged or don't-show). Possible values:
:PROBABLE-ENZYME -- the user should try to find a reaction to match to this protein
:AMBIGUOUS -- multiple reaction assignment possibilities were found by the name matcher
:NOT-AN-ENZYME -- even though the function name matches the criteria to be a probable enzyme, the user has decide that it is not
:NON-SPECIFIC-ENZYME-NAME -- no reaction can be assigned because the function name is not specific enough
:DONT-SHOW -- the user has decided that this protein cannot be assigned to a reaction for the time being (reasons can be unspecified
or detailed in the FUNCTIONAL-ASSIGNMENT-COMMENT slot)
:FLAGGED -- this protein should be considered high-priority
VALUE-TYPE: (ONE-OF PROBABLE-ENZYME AMBIGUOUS NON-SPECIFIC-ENZYME-NAME NOT-AN-ENZYME DONT-SHOW FLAGGED)
DOMAIN: Polypeptides
GENE The gene that encodes the current polypeptide (or RNA).

When a polypeptide exists in one or more chemically modified forms, all of those forms of the polypeptide should link to the same gene frame using the Gene slot.

INVERSE: PRODUCT
VALUE-TYPE: Genes
DOMAIN: Polypeptides, tRNAs, rRNAs
GENETIC-CODE-NUMBER The NCBI translation table number (1-15) for the chromosome's genetic code. If no value is supplied, the standard genetic code (1) is assumed. The genetic codes are as follows:

1. Standard 2. Vertebrate Mitochondrial 3. Yeast Mitochondrial 4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5. Invertebrate Mitochondrial 6. Ciliate, Dasycladacean and Hexamita (no tables 7 or 8) 9. Echinoderm Mitochondrial 10. Euplotid Nuclear 11. Bacterial (same as standard, except for different alternate initiation codons) 12. Alternative Yeast Nuclear 13. Ascidian Mitochondrial 14. Flatworm Mitochondrial 15. Blepharisma Nuclear

See http://anatomy.med.unsw.edu.au/CBL/embryo/DNA/Genetic_Codes.htm for more info, including systematic ranges for each code and citations.

CARDINALITY: 1
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: INTEGER
DOMAIN: Genetic-Elements
GENOME A list of all chromosomes and plasmids in the genome of the organism. VALUE-TYPE: Genetic-Elements
DOMAIN: Organisms
GIBBS-0 The standard Gibbs free energy of formation of the compound. The values are in units of kcal/mol, assuming the common state in aqueous solution at pH=7 and T=25C. VALUE-TYPE: NUMBER
DOMAIN: Compounds
QUERYABLE?: T
GROUP-MEMBERS Values are the member genes of this paralogous gene group INVERSE: IN-PARALOGOUS-GENE-GROUP
VALUE-TYPE: Genes
DOMAIN: Paralogous-Gene-Groups
HISTORY Contains a textual history of changes made to this frame. Each item is either a string or a note frame. INHERITANCE-TYPE: UNIQUE
INVERSE: REFERENT-FRAMES
VALUE-TYPE: (OR STRING Notes)
DOMAIN: THING
COLLECTION-TYPE: LIST
HYPOTHETICAL-REACTIONS A list of reactions in this pathway that are considered hypothetical, probably because presence of the enzyme, reactants, or products have not been demonstrated. VALUE-TYPE: Reactions
DOMAIN: Pathways
QUERYABLE?: T
IN-PARALOGOUS-GENE
-GROUP
Links a gene to the paralogous gene groups of which that gene is a member. Each group describes a set of paralogous genes. INVERSE: GROUP-MEMBERS
VALUE-TYPE: Paralogous-Gene-Groups
DOMAIN: All-Genes
IN-PATHWAY This slot specifies the pathways that a reaction occurs in. INVERSE: REACTION-LIST
VALUE-TYPE: Pathways
DOMAIN: Generalized-Reactions
QUERYABLE?: T
INHIBITORS Values of this slot are tuples containing a transcription factor and a DNA binding site. Presence of the transcription factor bound to the DNA binding site inhibits this RNA-Polymerase binding reaction, and therefore inhibits transcription. VALUE-TYPE: SEXPR
DOMAIN: Binding-Reactions
INHIBITORS-ALL The computed set of all inhibitors of this enzymatic reaction as defined in all of the other inhibitors slots. READ-ONLY: T
GET-METHODS: GET-INHIBITORS-ALL
VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
INHIBITORS-ALLOSTERIC Allosteric inhibitors decrease the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that decreases the affinity of the enzyme to its substrates without affecting its VMAX. Allosteric inhibitors can be competitive or noncompetitive inhibitors, therefore, those inhibition categories can be used in conjunction with this category. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
INHIBITORS-COMPETITIVE Competitive inhibitors are compounds that competitively inhibit the specified enzyme activity by binding reversibly to the enzyme and preventing the substrate from binding. Binding of the inhibitor and substrate are mutually exclusive because it is assumed that the inhibitor and substrate can both bind only to the free enzyme. A competitive inhibitor can either bind to the active site of the enzyme, directly excluding the substrate from binding there, or it can bind to another site on the enzyme, altering the conformation of the enzyme such that the substrate can not bind to the active site. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
INHIBITORS-IRREVERSIBLE Irreversible inhibitors are compounds that irreversibly inhibit the specified enzyme activity by binding to the enzyme and dissociating so slowly that it is considered irreversible. For example, alkylating agents, such as iodoacetamide, irreversibly inhibit the catalytic activity of some enzymes by modifying cysteine side chains. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
INHIBITORS-NONCOMPETITIVE Noncompetitive inhibitors are compounds that noncompetitively inhibit the specified enzyme by binding reversibly to both the free enzyme and to the enzyme-substrate complex. The inhibitor and substrate may be bound to the enzyme simultaneously and do not exclude each other. However, only the enzyme-substrate complex (not the enzyme- substrate-inhibitor complex) is catalytically active. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
INHIBITORS-OTHER Compounds that inhibit the specified enzyme activity by a mechanism that has been characterized, but that cannot be clearly classified as irreversible, competitive, noncompetitive, uncompetitive, or allosteric. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
INHIBITORS-UNCOMPETITIVE Uncompetitive inhibitors are compounds that uncompetitively inhibit the specified enzyme activity by binding reversibly to the enzyme-substrate complex but not to the enzyme alone. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
INHIBITORS-UNKMECH Compounds that inhibit the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper(s) curated thus far do not define the mechanism, and a full literature search has yet to be performed. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
INSTANCE-NAME-TEMPLATE This slot is used to store a template pattern for automatic generation of new instance names. The slot is typically given a value in a class frame to indicate how names for all instances of that class should be generated. For example, the template "G0-*" would indicate that names for instances of the class should begin with "G0-", followed by a unique integer. DOMAIN: Paralogous-Gene-Groups
INTERRUPTED? The value of this slot is T for genes that are interrupted, i.e., those that have a stop codon inserted in the gene. A given interrupted gene will be described by two gene frames that describe the two halves of the gene.

CARDINALITY: 1
VALUE-TYPE: BOOLEAN
DOMAIN: All-Genes
QUERYABLE?: T
INVERSE DOMAIN: DOMAIN-SLOTS
ISOZYME-SEQUENCE
-SIMILARITY
Values are of the form (other-polypeptide YES/NO) VALUE-TYPE: LIST
DOMAIN: Proteins
KINETIC-CONSTANT VALUE-TYPE: NUMBER
DOMAIN: Reactions
QUERYABLE?: T
LAST-NAME The last name of this person. VALUE-TYPE: STRING
DOMAIN: People
CARDINALITY-MAX: 1
LAYOUT-ADVICE A set of keyword-value pairs that advise the pathway layout algorithms how best to lay out the pathway. Currently supported advice keywords are:

:CYCLE-TOP-CPD -- The advice is a compound key. In pathways containing a cycle, the cycle will be rotated so that the specified comound is positioned at twelve o'clock.

:CASCADE-RXN-ORDERING -- The advice is a list of reactions that form a partial order for reactions in a cascade pathway (i.e. the 2-component signalling pathways).

VALUE-TYPE: SEXPR
DOMAIN: Pathways
LEFT The compounds produced by this reaction. The coefficients of these compounds that are not equal to 1 are stored in annotations on the values of this slot, under the annotation label COEFFICIENT. INHERITANCE-TYPE: UNIQUE
INVERSE: APPEARS-IN-LEFT-SIDE-OF
VALUE-TYPE: (OR Chemicals Polymer-Segments STRING)
DOMAIN: Reactions
QUERYABLE?: T
LEFT-END-POSITION This slot encodes the left end (the end closer to the index origin for the coordinate system) nucleotide position for a DNA region. The value could be a real number in the case where the position is a point that lies in between two integer coordinates. MAXIMUM-CARDINALITY: 1
NUMERIC-MINIMUM: 0
VALUE-TYPE: INTEGER
DOMAIN: Polymer-Segments
UNITS: BASE-PAIRS
QUERYABLE?: T
LINKAGE-TYPE Indicates which kind of atom on the amino acid residue is bonded to the modifying group. VALUE-TYPE: (ONE-OF C-LINKED O-LINKED N-LINKED S-LINKED)
DOMAIN: Amino-Acid-Binding-Sites
LOCAL-KB-ORGID The Pathway Tools orgid for databases that are Pathway/Genome Databases (e.g. META for MetaCyc, ECOLI for EcoCyc). VALUE-TYPE: SYMBOL
DOMAIN: Databases
LOCATIONS This slot describes the one or more cellular locations in which this protein is found. VALUE-TYPE: (ONE-OF CYTOPLASM PERIPLASM MEMBRANE INNER-MEMBRANE OUTER-MEMBRANE MITOCHONDRIA MITOCHONDRIAL-MEMBRANE CHROMOPLAST PLASTID PLASTID-STROMA PLASTID-OUTER-MEMBRANE PLASTID-INNER-MEMBRANE PLASTID-INTERMEMBRANE-SPACE PLASTID-THYLAKOID CHLOROPLAST CHLOROPLAST-OUTER-MEMBRANE CHLOROPLAST-INNER-MEMBRANE CHLOROPLAST-INTERMEMBRANE-SPACE CHLOROPLAST-THYLAKOID MICROSOME ER CIS-GOLGI GOLGI TRANS-GOLGI VACUOLE TONOPLAST NUCLEUS NUCLEAR-OUTER-MEMBRANE NUCLEAR-INNER-MEMBRANE PERINUCLEAR-SPACE NUCLEOLUS PLASMALEMMA CELL-WALL PEROXISOME GLYOXYSOME)
DOMAIN: Proteins
QUERYABLE?: T
M-NAME DOMAIN: NIL
MEDLINE-UID This slot lists the Medline unique identifer associated with this publication (valid only for publications that are indexed in Medline). MAXIMUM-CARDINALITY: 1
NUMERIC-MINIMUM: 0
VALUE-TYPE: INTEGER
DOMAIN: Publications
MESH-HEADINGS This slot lists one or more MeSH (Medical Subject Headings) keywords that are associated with an article. VALUE-TYPE: STRING
DOMAIN: Publications
MIDDLE-NAME The middle name of this person. VALUE-TYPE: STRING
DOMAIN: People
MODIFIED-FORM This slot indicates proteins that are derived from the current protein by some type of chemical modification. INVERSE: UNMODIFIED-FORM
VALUE-TYPE: Proteins
DOMAIN: Proteins
QUERYABLE?: T
MOLECULAR-WEIGHT This slot lists the molecular weight of a chemical, in daltons. MAXIMUM-CARDINALITY: 1
NUMERIC-MINIMUM: 0
INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: NUMBER
DOMAIN: Chemicals
DIGITS-OF-PRECISION: 5
UNITS: DALTONS
QUERYABLE?: T
MOLECULAR-WEIGHT
-EXP
An experimentally determined molecular weight. When multiple values are stored in this slot they should be treated as alternative observations. NUMERIC-MINIMUM: 0
VALUE-TYPE: NUMBER
DOMAIN: Proteins
UNITS: KDALTONS
MOLECULAR-WEIGHT
-KD
Molecular weights for this molecule in kilodaltons. Values of this slot are computed by combining the values of the slots molecular-weight-seq and molecular-weight-exp. When multiple values are stored in this slot they should be treated as alternative observations. NUMERIC-MINIMUM: 0
READ-ONLY: T
GET-METHODS: GET-MW-KD
VALUE-TYPE: NUMBER
DOMAIN: Proteins
DIGITS-OF-PRECISION: 5
UNITS: KDALTONS
QUERYABLE?: T
MOLECULAR-WEIGHT
-SEQ
A molecular weight as computed from a nucleotide sequence. When multiple values are stored in this slot they should be treated as alternative observations. NUMERIC-MINIMUM: 0
VALUE-TYPE: NUMBER
DOMAIN: Proteins
DIGITS-OF-PRECISION: 5
UNITS: KDALTONS
MOVED-IN Compounds transported into the cell. VALUE-TYPE: Chemicals
DOMAIN: Transport-Reactions
MOVED-OUT Compounds transported out of the cell. VALUE-TYPE: Chemicals
DOMAIN: Transport-Reactions
N+1-NAME For a polymeric compound, the name to use when displaying it in its N+1 form VALUE-TYPE: STRING
DOMAIN: Chemicals
N-1-NAME For a polymeric compound, the name to use when displaying it in its N-1 form CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Chemicals
N-NAME For a polymeric compound, the name to use when displaying it in its N form VALUE-TYPE: STRING
DOMAIN: Chemicals
NAME-SLOT To be used only as an annotation on values of the slots LEFT and RIGHT in reaction frames, to say which name (defaults to COMMON-NAME) to use in displays. HIDE-SLOT?: T
NAMES This is a computed slot that returns the union of all names of this frame, by appending names from all other name slots. READ-ONLY: T
GET-METHODS: GET-NAMES
VALUE-TYPE: STRING
DOMAIN: Polymer-Segments, Organisms, Generalized-Reactions, Enzymatic-Reactions, Chemicals, Databases
QUERYABLE?: T
NEIDHARDT-SPOT
-NUMBER
This slot lists the Neidhardt Spot Number of the protein, reflecting its electrophoretic behavior in two-dimensional electrophoresis. VALUE-TYPE: STRING
DOMAIN: Proteins
QUERYABLE?: T
NET-REACTION-EQUATION This slot specifies the net chemical transformation accomplished by a pathway, including the stoichiometry, and is written in the form of a reaction equation. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Pathways
QUERYABLE?: T
TEMPLATE-FORMATING-FN: #'GEN-RXN-EQN
NEXT-IN-THREAD This slot is used to implement a threaded conversation by creating a doubly linked list of a set of notes. This slot implements the forward link in the doubly linked list. INVERSE: PREVIOUS-IN-THREAD
VALUE-TYPE: Notes
DOMAIN: Notes
OFFICIAL-EC? The value of this slot is NO if the current reaction either was not defined by the enzyme commission at all, or if the current equation stored for that reaction is not the equation assigned by the EC (such as if we have corrected the EC equation). Otherwise, the value is YES, which is the default inherited value. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: BOOLEAN
DOMAIN: Reactions
QUERYABLE?: T
ORIGINAL-FRAME
-TYPE
DOMAIN: 3-KETOACYL-COA, TETRADEHYDROACYL-COA, L-3-HYDROXYACYL-COA, D-3-HYDROXYACYL-COA, ACYL-COA
OVERVIEW-NODE-SHAPE Describes how an object should be drawn in the overview graph CARDINALITY: 1
VALUE-TYPE: (ONE-OF CIRCLE SQUARE TRIANGLE DIAMOND ELLIPSE-VERT ELLIPSE-HORIZ RECTANGLE-HORIZ RECTANGLE-VERT UPSIDE-DOWN-TRIANGLE)
DOMAIN: Polymer-Segments, Chemicals
HIDE-SLOT?: T
PATHWAY-INTERACTIONS This slot holds a comment that describes interactions between this pathway and other biochemical pathways, such as those pathways that supply an important precurser. VALUE-TYPE: STRING
DOMAIN: Pathways
PATHWAY-LINKS Each value is of the form (compound other-pathway*) where compound is a compound in the current pathway and all the other-pathways. If no other-pathways are specified, then all other pathways that contain compound are implied. VALUE-TYPE: LIST
DOMAIN: Pathways
PERTAINS-TO This slot lists the one or more classes that this evidence code pertains to. For example, some evidence codes pertain to promoters only. If no class is listed, we assume the evidence code pertains to all classes of objects. DOMAIN: Evidence
PGDB-AUTHORS A list of the names of the authors of this KB. The names will be displayed on a summary page for this organism. It is appropriate to suffix each name with the author's institution, e.g., "John Doe, University of New Jersey". Use one slot value per author. VALUE-TYPE: STRING
DOMAIN: Organisms
PGDB-COPYRIGHT The contents of this slot should be a copyright notice for this database. The copyright notice should preferably fit in one line because it will be printed at the bottom of every web page served for this organism database by the Pathway Tools WWW server. Example: Copyright 1999 University of XXX. CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Organisms
PGDB-FOOTER-CITATION The value of this slot should be a single literature citation, in the form of a string, such as "Bioinformatics 12:155 2002". This citation, if present, will be printed at the bottom of each web page served for this organism, within the following text:

Please cite XXXCyc as CITATION in publications resulting from its use.

CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Organisms
PGDB-HOME-PAGE The URL of a WWW page describing this PGDB. This page can be used by the authors to provide more background information about the PGDB. CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Organisms
PGDB-NAME The name of the database for this organism, when the database name is to be printed somewhere by the Pathway Tools. Examples: "EcoCyc", "PlasmoCyc". The suffix "Cyc" is not required. CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Organisms
PGDB-UNIQUE-ID A string that serves as a unique ID for this PGDB to differentiate it from other PGDBs. This ID is used to build unique IDs for newly created frames that are created in this PGDB so that (a) when frames are copied among PGDBs, we know what PGDB the frame originated in, and (b) we can help to ensure that two frames in two different PGDBs that have the same ID do in fact refer to the same biological entity. The MetaCyc KB has a PGDB-Unique-ID of NIL; all other KBs should have a non-NIL value for this slot. These IDs should be short, and are encoded using base 36, e.g., "0" "1A" "D3".

CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Organisms
PGDB? True if the database is a Pathway/Genome Database that uses the Pathway Tools schema. CARDINALITY: 1
VALUE-TYPE: BOOLEAN
DOMAIN: Databases
PHYSIOLOGICALLY
-RELEVANT
This slot is a companion to all slots that describe activators and inhibitors. It contains a list of those activators and inhibitors whose effects are known to be of physiological relevance. The values of this slot are therefore a (possibly empty) subset of all values of the activators and inhibitors slots. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
PI Stores the pI of a polypeptide. When multiple values are stored in this slot they should be treated as alternative observations. NUMERIC-MINIMUM: 0
NUMERIC-MAXIMUM: 14
VALUE-TYPE: NUMBER
DOMAIN: Polypeptides
QUERYABLE?: T
PKA1 Ionization constant of the first site in this compound to ionize. VALUE-TYPE: NUMBER
DOMAIN: Compounds
QUERYABLE?: T
PKA2 Ionization constant of the second site in this compound to ionize. VALUE-TYPE: NUMBER
DOMAIN: Compounds
QUERYABLE?: T
PKA3 Ionization constant of the third site in this compound to ionize. VALUE-TYPE: NUMBER
DOMAIN: Compounds
QUERYABLE?: T
POLYMERIZATION
-LINKS
Each value of this slot is of the form (cpd-class product-rxn reactant-rxn). When both reactions are non-nil, an identity link is created between the polymer compound class cpd-class, a product of product-rxn, and the same compound class as a reactant of reactant-rxn. The PRODUCT-NAME-SLOT and REACTANT-NAME-SLOT annotations specify which slot should be used to derive the compound label in product-rxn and reactant-rxn above respectively --- if one or both are omitted, COMMON-NAME is assumed. Either reaction above may be nil; in this case, no identity link is created --- this form is used solely in conjunction with one of the name-slot annotations to specify a name-slot other than COMMON-NAME for a polymer compound class in a reaction of the pathway. DOMAIN: Pathways
POSSIBLE-FEATURE
-STATES
For a given feature class, this slot describes the possible states available to instances of the class. For example, a feature that represents a binding-site can have either a bound or unbound state. The list of possible states is stored at the class level as values for this slot. A particular instance of the class (a specific feature of a specific protein) can then be labeled with this state information using the STATE annotation when it appears in the FEATURES slot of the protein. For example, two forms of the same protein would link to the same feature, but one form might have the feature annotated with the bound label, whereas the other might label the feature as unbound. DOMAIN: Protein-Features
PREDECESSORS This slot describes the linked reactions that comprise the current pathway. Each value of this slot is of the form (reaction-id pred-id*). Each pred-id is the id of a reaction frame that is a direct predecessor of reaction-id in the pathway. VALUE-TYPE: SEXPR
DOMAIN: Pathways
PREVIOUS-IN-THREAD This slot is used to implement a threaded conversation of a series of notes as a doubly linked list of notes. This slot implements the backward link in the doubly linked list. INVERSE: NEXT-IN-THREAD
VALUE-TYPE: Notes
DOMAIN: Notes
PRIMARIES When drawing a pathway, EcoCyc usually computes automatically which compounds are primaries (mains) and which compounds are secondaries (sides). Occasionally, the heuristics we use are not sufficient to make the correct distinction. This slot is used to specify a list of primary reactants, primary products, or both for a particular reaction in the pathway. Values are of the form (reaction-id
(primary-reactant-id-1 ... primary-reactant-id-n)
(primary-product-id-1 ... primary-product-id-n) )
VALUE-TYPE: LIST
DOMAIN: Pathways
PRIORITY VALUE-TYPE: INTEGER
DOMAIN: Notes
CARDINALITY-MAX: 1
PRIVATE? A slotunit whose Private? slot is set to T indicates that the slot contains private data for PGDB developers only, which should not be visible in public views of the PGDB. For example, private slots will not be included in KB dumps. This slot should not be confused with the Private? field in the orgkb defstruct, which indicates whether a PGDB is private. DOMAIN: DOMAIN-SLOTS
PRODUCT This slot lists the product of a gene, which could be a polypeptide or a tRNA. Multiple products will be recorded in the case that several chemically modified forms of the protein product exist. INVERSE: GENE
VALUE-TYPE: (OR Polypeptides RNA)
DOMAIN: All-Genes
QUERYABLE?: T
PRODUCT-NAME-SLOT To be used only as an annotation on values of the slot POLYMERIZATION-LINKS: contains the name of a slot (e.g. COMMON-NAME, N+1-NAME, N-1-NAME) that is used to get the name of a compound when it is a product of the reaction to which this annotation is attached in the pathway frame. HIDE-SLOT?: T
PRODUCT-STRING This slot holds a text string that describes the product of this gene; this slot is only used when EcoCyc does not describe the gene product as a frame (such as a polypeptide frame). VALUE-TYPE: STRING
DOMAIN: All-Genes
QUERYABLE?: T
PRODUCT-TYPES Describes the type of the gene product, e.g., is it an enzyme, an RNA, etc. VALUE-TYPE: (ONE-OF ENZYME REGULATOR LEADER MEMBRANE TRANSPORT STRUCTURAL RNA PHENOTYPE FACTOR CARRIER ORF EXTRACHROMOSOMAL-ELEMENT)
DOMAIN: All-Genes
PROSTHETIC-GROUPS Prosthetic groups are compounds that are required for an enzyme to catalyze a reaction, but that are unchanged by the reaction, and that are covalently or tightly bound to the enzyme. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
PTOOLS-VERSION This slot is used in the KB-DESCRIPTOR frame to specify the version of PTools that was used to write this PGDB, that is, the version of PTools for which this PGDB is valid. DOMAIN: KB-DESCRIPTOR
PUBMED-ID The PubMed unique ID for publications indexed by PubMed. VALUE-TYPE: INTEGER
DOMAIN: Publications
QUERYABLE? Defines whether a slot is queryable using the Genopath WWW query interface. Slots for which Queryable? is marked as NIL will not appear in that query interface. CARDINALITY: 1
VALUE-TYPE: BOOLEAN
DOMAIN: SLOTS
REACTANTS The compounds to be bound by this reaction. INVERSE: APPEARS-IN-BINDING-REACTIONS
VALUE-TYPE: (OR Chemicals Polymer-Segments STRING)
DOMAIN: Binding-Reactions
REACTION The value of this slot is the key of a frame from the Reaction class -- the second half of the enzyme/reaction pair that the current frame describes. In fact, this slot can have multiple values corresponding to multiple reactions catalyzed by a single catalytic site of an enzyme. MINIMUM-CARDINALITY: 1
INVERSE: ENZYMATIC-REACTION
VALUE-TYPE: Reactions
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
REACTION-DIRECTION Specifies the directionality of a reaction. This slot is particularly important to fill for reactions that are not part of a pathway, because for such reactions, the direction cannot be computed automatically, whereas for reactions within a pathway, the direction can be inferred from the pathway context.

Possible values of this slot are:

REVERSIBLE: Reaction occurs in both directions in physiological settings.

PHYSIOL-LEFT-TO-RIGHT PHYSIOL-RIGHT-TO-LEFT The reaction occurs in the specified direction in physiological settings, because of several possible factors including the energetics of the reaction, local concentrations of reactants and products, and the regulation of the enzyme or its expression.

IRREVERSIBLE-LEFT-TO-RIGHT IRREVERSIBLE-RIGHT-TO-LEFT For all practical purposes, the reaction occurs only in the specified direction in physiological settings, because of chemical properties of the reaction.

CARDINALITY: 1
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: (ONE-OF REVERSIBLE PHYSIOL-LEFT-TO-RIGHT PHYSIOL-RIGHT-TO-LEFT IRREVERSIBLE-LEFT-TO-RIGHT IRREVERSIBLE-RIGHT-TO-LEFT)
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
REACTION-LIST This slot lists all reactions in the current pathway, in no particular order. It is automatically computed from the predecessors slot. INVERSE: IN-PATHWAY
VALUE-TYPE: Generalized-Reactions
DOMAIN: Pathways
QUERYABLE?: T
REACTION-PRESENT
-IN-E-COLI?
This slot is no longer used in the KB, but it is used in templates and so its slotunit must be kept MAXIMUM-CARDINALITY: 1
VALUE-TYPE: BOOLEAN
DOMAIN: Reactions
HIDE-SLOT?: T
RECIPIENTS A list of the People frames identifying the recipients of this note. VALUE-TYPE: People
DOMAIN: Notes
REFERENT-FRAME If a publication is a synonym frame, the value of this slot is the frame containing the actual data. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: Publications
DOMAIN: Publications
REFERENT-FRAMES Contains a list of one or more frames that this note refers to. INVERSE: HISTORY
VALUE-TYPE: THING
DOMAIN: Notes
REGULATED-PROMOTER Along with the slot RELATIVE-CENTER-DISTANCE, this slot is used to determine the absolute location of the binding site -- i.e. the relative-center-distance represents the position of the site relative to the promoter specified in this slot. The binding site is assumed to regulate this promoter, but it may regulate other promoters not specified in this slot, as well (as this slot is single-valued). CARDINALITY: 1
VALUE-TYPE: Promoters
DOMAIN: DNA-Binding-Sites
RELATIVE-CENTER
-DISTANCE
This slot defines the distance from the center of this binding site to the promoter specified in the REGULATED-PROMOTER slot. A negative value means that the site is upstream from the promoter, and a positive value means that the site is downstream from the promoter. CARDINALITY: 1
VALUE-TYPE: NUMBER
DOMAIN: DNA-Binding-Sites
REQUIRED-PROTEIN
-COMPLEX
Some enzymes only catalyze a particular reaction when they are components of a larger protein complex. For such an enzyme, this slot identifies the particular protein complex of which the enzyme must be a component. VALUE-TYPE: Protein-Complexes
DOMAIN: Enzymatic-Reactions
QUERYABLE?: T
REQUIREMENTS Analogous to cofactors, but for non-enzymatic reactions. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Reactions
QUERYABLE?: T
RESIDUE-NUMBER The numeric index of the amino acid residue or residues that make up this site. Number 1 corresponds to the N-terminal amino acid. VALUE-TYPE: INTEGER
DOMAIN: Amino-Acid-Sites
RESIDUE-TYPE The identity of the amino acid residue or residues that make up this site. VALUE-TYPE: Amino-Acids
DOMAIN: Amino-Acid-Sites
RESOLVING-PERSON The person, if any, who resolved the issue raised by this note. VALUE-TYPE: People
DOMAIN: Notes
CARDINALITY-MAX: 1
RIGHT The compounds consumed by this reaction. The coefficients of these compounds that are not equal to 1 are stored in annotations on the values of this slot, under the annotation label COEFFICIENT. INHERITANCE-TYPE: UNIQUE
INVERSE: APPEARS-IN-RIGHT-SIDE-OF
VALUE-TYPE: (OR Chemicals Polymer-Segments STRING)
DOMAIN: Reactions
QUERYABLE?: T
RIGHT-END-POSITION This slot encodes the right end (the end closer to the index origin for the coordinate system) nucleotide position for a DNA region. The value could be a real number in the case where the position is a point that lies in between two integer coordinates. MAXIMUM-CARDINALITY: 1
NUMERIC-MINIMUM: 0
VALUE-TYPE: INTEGER
DOMAIN: Polymer-Segments
UNITS: BASE-PAIRS
QUERYABLE?: T
SCHEMA DOMAIN: EC-1.21.99
SCHEMA? This slot is used to indicate which KB classes are logically part of the general GenoPath (MetaCyc) schema (are organism-independent), in contrast to those slots that are specific to a particular organism.

This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring.

The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions.

MAXIMUM-CARDINALITY: 1
INHERITANCE-TYPE: OVERRIDE
VALUE-TYPE: BOOLEAN
DOMAIN: THING
SEARCH-OBJECT-CLASS This slot lists the classes of EcoCyc objects (e.g. Pathways, Genes, Proteins, etc.) that can have unification links to this database via the search URL. DOMAIN: Databases
SEEN-BY A list of those recipients of this note who have actually read the note. VALUE-TYPE: People
DOMAIN: Notes
SEEN-NOTES A list of the notes this person has read. VALUE-TYPE: Notes
DOMAIN: People
SENDER The person who sent this note, implemented as an instance of the class People. VALUE-TYPE: People
DOMAIN: Notes
CARDINALITY-MAX: 1
SEQUENCE-FILE Filename containing the full chromosome sequence in FASTA fo rmat CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Chromosomes
SEQUENCE-LENGTH Length of a genetic element in bases. NUMERIC-MINIMUM: 1000
VALUE-TYPE: INTEGER
DOMAIN: Genetic-Elements
CARDINALITY: 1
SIGNAL Environmental signal that triggers this reaction. Typically this signal is a small molecule, however, the signal can also be a string because in some cases we wish to denote a signal in an uncontrolled way to encode imprecise biological knowledge. VALUE-TYPE: (OR Compounds STRING)
DOMAIN: Reactions
QUERYABLE?: T
SMILES A smiles string for this compound, computed automatically from the compound structure. READ-ONLY: T
GET-METHODS: GET-SMILES
VALUE-TYPE: STRING
DOMAIN: Compounds
SOURCE This slot lists the source in which a given publication occurs, such as the name of a journal and its volume and page numbers. The syntax of this slot is not strictly controlled. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Publications
SPECIES This slot is used in three ways: 1) In pathway frames in MetaCyc: its values are organisms in which the pathway is known to occur (not necessarily an exhaustive list, however). 2) In protein frames in MetaCyc: it is usually single-valued, and names the species whose protein the frame describes. 3) In reaction frames in organism KBs: If a reaction has no enzymatic-reaction frame (i.e. no information about the enzyme is known), but is known to
occur in the organism nevertheless, then this slot should contain a single value, the ID for the current organism.
VALUE-TYPE: (OR Organisms STRING)
DOMAIN: Reactions, Pathways, Proteins
QUERYABLE?: T
SPLICE-FORM-INTRONS Lists the introns for the splice form of the gene that codes for this particular polypeptide or RNA. Because different splice forms of a given gene will give rise to different proteins or RNAs, the list of introns is associated with the end product of the splice form (the protein or RNA) rather than with the gene. Each value of this slot is a two-element list (start-bp end-bp), containing the start and end position of an intron, respectively. Positions refer to base pair numbers relative to the start of the gene, with the first base pair (if the gene is transcribed in the negative direction, this is the first base pair of the reverse complement) being number 1. Start-bp and end-bp are included as part of the intron. Introns cannot overlap, start-bp must be less than end-bp, and neither start-bp nor end-bp can be less than 1 or greater than the length of the gene. If a splice form has a different start position than the gene as a whole, then it should specify an intron extending from 1 to its start position. Similarly, if it has a different end position, an extra intron should be specified there. VALUE-TYPE: LIST
DOMAIN: RNA, Polypeptides
SPONTANEOUS? Does the reaction occur spontaneously in vivo, without catalysis by an enzyme? MAXIMUM-CARDINALITY: 1
VALUE-TYPE: BOOLEAN
DOMAIN: Generalized-Reactions
QUERYABLE?: T
STATIC-SEARCH-URL Stores URL format string for OID searches. Format string has one arg: the desired OID. VALUE-TYPE: STRING
DOMAIN: Databases
STATUS Indicates the status of a note as new, read, flagged, etc. As far as pkarp can tell, no code utilizing this slot has been written. DOMAIN: Notes
STIMULATORS Compounds or proteins known to stimulate a non-enzymatic reaction. Often the mechanism is unknown -- the action may even be indirect. VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Reactions
QUERYABLE?: T
STRAIN-NAME Specifies the strain name for the organism. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: Organisms
STRUCTURE-ATOMS This slot is one of several that are used to encode the chemical structure of a compound. This slot lists all of the distinct atoms in the compound, with multiple entries for atoms of the same element that occur more than once. For example, water could be described as the list (H H O). There is no special order in which the atoms are listed. However, other slots refer to the atoms in the compound according to their position in this list, for example, the first hydrogen is atom 0, and the oxygen is atom 2. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: (OR Elements Groups Proteins)
DOMAIN: Chemicals
HIDE-SLOT?: T
COLLECTION-TYPE: LIST
STRUCTURE-BONDS This slot describes the chemical bonds within a compound. Each bond is encoded as a list of the form (A1 A2 B-TYPE) where A1 is the index in slot Structure-Atoms of the first atom in the bond, A1 is the index of the second atom in the bond, and B-TYPE encodes the type of the chemical bond. Valid bond types are the numbers 1, 2, and 3 for single, double, and triple bounds, and the symbol :AROMATIC for aromatic bonds. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: LIST
DOMAIN: Chemicals
HIDE-SLOT?: T
COLLECTION-TYPE: LIST
SUB-PATHWAYS This slot lists all the direct sub-pathways of a pathway. INVERSE: SUPER-PATHWAYS
VALUE-TYPE: Pathways
DOMAIN: Pathways
QUERYABLE?: T
SUBJECT Contains the subject line for this note. VALUE-TYPE: STRING
DOMAIN: Notes
CARDINALITY-MAX: 1
SUBREACTIONS Values form a list of component reactions, the sum of whose reaction equations should add up to the equation of the parent reaction VALUE-TYPE: Reactions
DOMAIN: Reactions
SUBSTRATES The union of the reactants and products of the reaction. READ-ONLY: T
GET-METHODS: GET-SUBSTRATES
VALUE-TYPE: (OR Chemicals STRING)
DOMAIN: Reactions
QUERYABLE?: T
SUPER-PATHWAYS This slot lists direct super-pathways of a pathway. It is computed by comparing the predecessors slots of each pathway in the KB. INVERSE: SUB-PATHWAYS
VALUE-TYPE: Pathways
DOMAIN: Pathways
QUERYABLE?: T
SUPERATOMS Indicates that part of the compound structure can be replaced by a superatom. The annotations REPLACES-ATOM AND CONNECTED-TO specify which atom (by indexing into the STRUCTURE-ATOMS list) the superatom replaces, and which atom in the compound structure it is connected to, respectively. Superatoms may only connect at one atom. INHERITANCE-TYPE: UNIQUE
DOMAIN: Compounds
SYMMETRY This slot defines the type of symmetry found in the DNA binding site recognized by a transcription factor. The two possible symmetry types are INVERTED-REPEAT and DIRECT-REPEAT. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: (ONE-OF DIRECT-REPEAT INVERTED-REPEAT ASYMMETRIC)
DOMAIN: Proteins
SYNONYM-SLOTS This slot in the KB-DESCRIPTOR lists the one or more slots in which names of the entity that a frame represents are stored. A typical value of this slot is the list '(COMMON-NAME SYNONYMS). This slot is used by code that searches for frames by name so that it knows in a KB-independent fashion what slots to look in during that search. DOMAIN: KB-DESCRIPTOR
SYNONYMS One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: Polymer-Segments, Organisms, Generalized-Reactions, Enzymatic-Reactions, Chemicals
SYSTEMATIC-NAME This slot stores the systematic chemical name of a chemical. MAXIMUM-CARDINALITY: 1
INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: Compounds
TAXONOMIC-DOMAIN The taxonomic domain to which this organism belongs. The names used here are the same names used in Swiss-Prot and NCBI taxonomy as of November 2002. CARDINALITY: 1
VALUE-TYPE: (ONE-OF BACTERIA EUKARYOTA ARCHAEA VIRUSES)
DOMAIN: Organisms
TEMPLATE-FILE This outdated slot stores the template file (an outdated form of input to EcoCyc) from which a given frame was created. MAXIMUM-CARDINALITY: 1
INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: Polymer-Segments, Generalized-Reactions, Enzymatic-Reactions, Chemicals
HIDE-SLOT?: T
PRIVATE?: T
TEMPLATE-FORMATING
-FN
HIDE-SLOT?: T
TEMPLATE-NAME HIDE-SLOT?: T
TEXT Contains the text of the note. VALUE-TYPE: STRING
DOMAIN: Notes
TITLE This slot stores the title of a publication, such as the title of a book or article. VALUE-TYPE: STRING
DOMAIN: Publications
TRANSCRIPTION-DIRECTION This slot specifies the direction along the chromosome in which this gene is transcribed; allowable values are + or -. MAXIMUM-CARDINALITY: 1
VALUE-TYPE: (ONE-OF + -)
DOMAIN: All-Genes
QUERYABLE?: T
UNITS Defines the units of measure for a slot. CARDINALITY: 1
VALUE-TYPE: SYMBOL
DOMAIN: SLOTS
UNMODIFIED-FORM This slot allows a protein to point to its apo form, which must be another protein. The value of the Unmodified-Form slot is always the completely unmodified "base" form of a protein, that is, if a protein can undergo several subsequent stages of modification, each modified form is linked back to the base form, not to the previous form in the pathway.

Put another way, no protein should have both an unmodified form and a modified form; every modified protein should be linked back to the base form of the protein.

MAXIMUM-CARDINALITY: 1
INVERSE: MODIFIED-FORM
VALUE-TYPE: Proteins
DOMAIN: Proteins
QUERYABLE?: T
UNSEEN-NOTES A list of the notes this person has not yet read. VALUE-TYPE: Notes
DOMAIN: People
URL One or more URLs containing the referenced document. VALUE-TYPE: STRING
DOMAIN: Publications
VALENCE Valence applies to all-elements because superelements must have a valence. Some elements may have several valence possibilities, due to non-bonding electron pairs that can get oxydized. In such cases, the code that performs valence checking in order to draw hydrogens that fill unsatisfied valences will only fill up to the lowest valence value. VALUE-TYPE: NUMBER
DOMAIN: All-Elements
VARIANTS? This slot should be set in a pathway class whose purpose is to group together a set of variant pathways. Variant pathways are those that accomplish roughly the same biological function, such as degradation of a given starting material, or biosynthesis of an end product. The variant pathways may or may not share any common reactions. This slot distinguishes classes that group together a set of variant pathways from other pathway classes that are used to define the taxonomy of pathways. CARDINALITY: 1
INHERITANCE-TYPE: OWN
VALUE-TYPE: BOOLEAN
DOMAIN: Pathways
QUERYABLE?: NIL
VISIBLE-ROOT-MAP
-LOCI
This slot specifies a list of gene names or IDs that will be displayed as markers on the lowest-resolution view of the map of this genetic element.
VALUE-TYPE: DNA-Segments
DOMAIN: Genetic-Elements
YEAR The 4-digit year in which the publication was published VALUE-TYPE: INTEGER
DOMAIN: Publications