The set of words to remove from all keys to create a lookup key.
The set of words to remove from all keys to create a lookup key.
Filename of the auxiliary biological processes file.
Filename of the auxiliary biological processes file.
Filename of the auxiliary cellular location file.
Filename of the auxiliary cellular location file.
Filename of the auxiliary small molecule (chemical) file.
Filename of the auxiliary small molecule (chemical) file.
Filename of the auxiliary small molecule (metabolite) file.
Filename of the auxiliary small molecule (metabolite) file.
Filename of the auxiliary protein family file.
Filename of the auxiliary protein family file.
Filename of the auxiliary protein file.
Filename of the auxiliary protein file.
Filename of the auxiliary protein file.
Filename of the auxiliary protein file.
The set of words to remove from a key to create a protein family lookup key.
The set of words to remove from a key to create a protein family lookup key.
Filename of the cellular location file generated by the entity checker.
Filename of the cellular location file generated by the entity checker.
Prefix string for cellular location IDs generated by the entity checker.
Prefix string for cellular location IDs generated by the entity checker.
Filename of the small molecule file generated by the entity checker.
Filename of the small molecule file generated by the entity checker.
Prefix string for small molecule IDs generated by the entity checker.
Prefix string for small molecule IDs generated by the entity checker.
Filename of the protein/family file generated by the entity checker.
Filename of the protein/family file generated by the entity checker.
Prefix string for protein/family IDs generated by the entity checker.
Prefix string for protein/family IDs generated by the entity checker.
The set of words to remove from the text to create a lookup key.
The set of words to remove from the text to create a lookup key.
File Path to the directory which holds the entity knowledge bases.
File Path to the directory which holds the entity knowledge bases.
Resource Path to the directory which holds the entity knowledge bases.
Resource Path to the directory which holds the entity knowledge bases.
The set of characters to remove from the text to create a lookup key.
The set of characters to remove from the text to create a lookup key.
Filename of the manually maintained cellular location file.
Filename of the manually maintained cellular location file.
Filename of the manually maintained small molecule file.
Filename of the manually maintained small molecule file.
Filename of the manually maintained protein family file.
Filename of the manually maintained protein family file.
Filename of the manually maintained protein file.
Filename of the manually maintained protein file.
The set of words to remove from a key to create a protein lookup key.
The set of words to remove from a key to create a protein lookup key.
Filename of the static cellular location file.
Filename of the static cellular location file.
Filename of the static small molecule (chemical) file.
Filename of the static small molecule (chemical) file.
Filename of the static small molecule (chemical) file.
Filename of the static small molecule (chemical) file.
Filename of the static protein family file.
Filename of the static protein family file.
Filename of the static protein file.
Filename of the static protein file.
Filename of the static tissue type file.
Filename of the static tissue type file.
The primary URI of the external KB (e.g., http://identifiers.org/uniprot/).
The primary URI of the external KB (e.g., http://identifiers.org/uniprot/).
Extract and return a key string, from the given Mention, which can be used to access an external knowledge base or a local object cache.
Extract and return a key string, from the given Mention, which can be used to access an external knowledge base or a local object cache.
The namespace of the external KB (e.g., uniprot).
The namespace of the external KB (e.g., uniprot).
Using the given Mention, generate a URI which references an entry in the namespace of external knowledge base.
Using the given Mention, generate a URI which references an entry in the namespace of external knowledge base.
Using the given ID string, generate a URI which references an entry in the namespace of external knowledge base (e.g., given "P2345" => "http://identifiers.org/uniprot/P2345").
Using the given ID string, generate a URI which references an entry in the namespace of external knowledge base (e.g., given "P2345" => "http://identifiers.org/uniprot/P2345").
Overridden to perform alternate key lookups.
Overridden to perform alternate key lookups.
Resolve the given Mention to an entry in an external knowledge base, for any of the species name strings in the given set, and return a map of keys and property values from that entry.
Resolve the given Mention to an entry in an external knowledge base, for any of the species name strings in the given set, and return a map of keys and property values from that entry. NB: Default method ignores species argument and resolves to any species.
Resolve the given Mention to an entry in an external knowledge base, failing if the entry is not for humans, and return a map of keys and property values from that entry.
Resolve the given Mention to an entry in an external knowledge base, failing if the entry is not for humans, and return a map of keys and property values from that entry. NB: Default method ignores species argument and resolves to any species.
The Resource Identifier for the primary resource location for this knowledge base (e.g., MIR:00100164).
The Resource Identifier for the primary resource location for this knowledge base (e.g., MIR:00100164). NB: This is MIRIAM registration ID of the external knowledge base, NOT an entity ID.
For each of the given key transforms, try the KB lookup in sequence.
For each of the given key transforms, try the KB lookup in sequence. Return the optioned result from the first lookup which resolves a transformed key, or None otherwise.
KB accessor to resolve protein names via KBs generated from the BioPax model.