Additional constructor to add namespace to meta information for reference.
Type alias for functions which take a text string and return a potential key string.
Type alias for functions which take a text string and return a potential key string.
Species name sets.
Species name sets.
Add the given entry to this KB, if it is unique.
Return a sequence of alternate keys, one for each of the given key transforms.
Return a sequence of alternate keys, one for each of the given key transforms.
Tell whether the given sequence of namespace/ID strings contains a human nsId.
Tell whether the given sequence of namespace/ID strings contains a human nsId.
Tell whether the given sequence of species strings contain a human species label.
Tell whether the given sequence of species strings contain a human species label.
Return an sequence over the entries in this KB.
Tell whether the given namespace/ID string is an ID for humans or not.
Tell whether the given namespace/ID string is an ID for humans or not.
Check for one of several types of hyphen-separated strings and, if found, extract and return the candidate text portion, else return the text unchanged.
Check for one of several types of hyphen-separated strings and, if found, extract and return the candidate text portion, else return the text unchanged.
Tell whether the given species string is label for humans or not.
Tell whether the given species string is label for humans or not.
Tell whether the given species string is a member of the given set of species.
Tell whether the given species string is a member of the given set of species.
Return resolutions for the set of all KB entries for the given key.
Find the set of KB entries, for the given key, which match the given single species.
Find the set of KB entries, for the given key, which match the given single species. Returns resolutions for matching entries or None.
Finds the set of KB entries, for the given key, which contains a species in the given set of species.
Finds the set of KB entries, for the given key, which contains a species in the given set of species. Returns resolutions for matching entries or None.
Finds the set of KB entries, for the given key, which have humans as the species.
Finds the set of KB entries, for the given key, which have humans as the species. Returns resolutions for matching entries or None.
Find the set of KB entries, for the given key, which do not contain a species.
Find the set of KB entries, for the given key, which do not contain a species. Returns resolutions for matching entries or None.
Try lookups for all given keys until one succeeds or all fail.
Try lookups for all given keys until one succeeds or all fail.
Try lookups for all given keys until one succeeds or all fail.
Try lookups for all given keys until one succeeds or all fail.
Try lookups for all given keys until one succeeds or all fail.
Canonicalize the given text string into a key for both storage and lookup.
Canonicalize the given text string into a key for both storage and lookup.
Wrap the given optional KB entry in a new singleton-sequence of resolutions formed from this KB and the given KB entry.
Wrap the given KB entry in a new KB resolution formed from this KB and the given KB entry.
Wrap the given sequence of KB entries in a sequence of resolutions formed from this KB and the given KB entries.
Return alternate lookup keys created from the given text string and transform functions.
Return alternate lookup keys created from the given text string and transform functions.
Return the portion of the text string minus one of the protein family suffixes, if found in the given text string, else return the text lowercased.
Return the portion of the text string minus one of the protein family suffixes, if found in the given text string, else return the text lowercased.
Return the portion of the text string before a trailing mutation phrase, if found in the given text string, else return the text unchanged.
Return the portion of the text string before a trailing mutation phrase, if found in the given text string, else return the text unchanged.
Return the portion of the text string minus one of the organ-cell-type suffixes, if found in the given text string, else return the text unchanged.
Return the portion of the text string minus one of the organ-cell-type suffixes, if found in the given text string, else return the text unchanged.
Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return the text unchanged.
Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return the text unchanged.
Return the portion of the text string minus one of the protein suffixes, if found in the given text string, else return the text lowercased.
Return the portion of the text string minus one of the protein suffixes, if found in the given text string, else return the text lowercased.
Try to remove all of the suffixes in the given set from the given text.
Try to remove all of the suffixes in the given set from the given text.
The root data structure implementing this in-memory knowledge base.
Wrap the given KB entry in a new singleton-sequence of resolutions formed from this KB and the given KB entry.
Class implementing an in-memory knowledge base indexed by key and species. Written by: Tom Hicks. 10/25/2015. Last Modified: Add default sort-by-human for resolutions returned from IMKB.