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.
COMMENT: GeneCards[tm] is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
COMMENT: Technically, Swiss-Prot is a subset of UniProt. It is preferable to
link using the DBID UNIPROT, because linking via DBID SWISSPROT
assumes we know that a protein is in SwissProt as opposed to TrEMBL.
DBID SWISSPROT is provided for backward compatibility with
earlier BioCyc links that use that DBID. Because even in
the existing links it is possible that some links are really
to TrEMBL, I have changed the Common-Name slot in this frame
to be UniProtKB (PDK).
COMMENT: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
COMMENT: The Entrez-Gene Database allows reference to individual genes that were sequenced as part of a
genome sequencing project. The accession number of the genes in the database is referred to as a
Gene ID.
When references to Gene IDs are included in the annotated genome of an organism, the PathoLogic
component of Pathway Tools will create links to this database during the generation of the PGDB.
COMMENT: The objective of GO is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.
COMMENT: UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
COMMENT: This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information.
COMMENT: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
COMMENT: Wikipedia is a multilingual, web-based, free content
encyclopedia project, which is written collaboratively by volunteers from all around the world.
COMMENT: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
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).
An abbreviated name for the current frame. This slot can be used for virtually all classes; see
specification of the :Synonym-Slots for a given class to be sure. In particular, this name for
a database is displayed in DB-links, and in some author credit displays of an organization's name.
This slot attributes credit to various contributors, which can be individual people or organizations, or both.
The type of contribution is indicated by several types of annotation labels that are attached to the slot values,
each of them bearing numerical time-stamps as the values (in Common Lisp universal time format) that indicate
the approximate times of the contributions. The code dealing with author-crediting sets and shows
the timestamps with a precision of one day.
The legal slot values are frames of the |People| or |Organizations| classes, in any combination or order.
Each such contributor frame is assumed to occur only once in the slot.
As of Oct. 2005, the legal annotation labels are: CREATED REVIEWED REVISED LAST-CURATED .
For the annotation labels CREATED and LAST-CURATED , it only makes sense to store one timestamp,
but for the other labels, in general, arbitrarily many timestamps can be recorded.
An association between authors and organizations is assumed if they share the same credit event,
in terms of the same combination of annotation label and timestamp.
QUERYABLE?: T
DOMAIN: THING
VALUE-TYPE: (OR People Organizations)
INVERSE: CREDITED-FOR
INHERITANCE-TYPE: UNIQUE
COMMON-NAME: Credits
A string describing the data source from which this object was derived, such as the name of a
laboratory or a database. Used principally by the PTools BioPAX importer.
QUERYABLE?: T
DOMAIN: THING
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
COMMON-NAME: Data-Source
This slot contains a regular expression string defining legal values for links to this database.
The regular expression syntax is mostly compatible with Perl regular expression syntax, and
is described at http://franz.com/support/documentation/8.1/doc/regexp.htm#regexp-new-summary-2.
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 classes 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.
This slot lists the classes of PGDB objects (e.g. Pathways, Genes, Proteins, etc.) that can have unification links to this database via the search URL.
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.
QUERYABLE?: T
DOMAIN: THING
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
COMMON-NAME: Synonyms