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.
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 a sequence over the entries in this KB.
Return a 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.
Tell whether this KB contains species information or not.
Tell whether this KB contains species information 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.
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.
Return meta information about the external KB from which this KB was created.
Return meta information about the external KB from which this KB was created.
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.
Resolve the given Mention to an optional entry in a knowledge base.
Resolve the given Mention to an optional entry in a knowledge base. Return a resolution for the entry, if any found.
Resolve the given text string to an optional entry in a knowledge base.
Resolve the given text string to an optional entry in a knowledge base. Return a resolution for the entry, if any found.
Resolve the given Mention to an optional entry in a knowledge base.
Resolve the given Mention to an optional entry in a knowledge base. If the mention is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.
Resolve the given text string to an optional entry in a knowledge base.
Resolve the given text string to an optional entry in a knowledge base. If the text is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.
Resolve the given Mention to an optional entry in a knowledge base, for the single named species.
Resolve the given Mention to an optional entry in a knowledge base, for the single named species. Return a resolution for the entry, if any found.
Resolve the given text string to optional group of entries in a knowledge base, returning resolutions for all entries found in the KB, for the given species.
Resolve the given text string to optional group of entries in a knowledge base, returning resolutions for all entries found in the KB, for the given species.
Resolve the given Mention to an optional entry in a knowledge base, for the single named species.
Resolve the given Mention to an optional entry in a knowledge base, for the single named species. If the mention is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.
Resolve the given text string to an optional entry in a knowledge base, for the single named species.
Resolve the given text string to an optional entry in a knowledge base, for the single named species. If the text is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.
Resolve the given Mention to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.
Resolve the given Mention to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.
Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all entries found in the KB, with any of the given species.
Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all entries found in the KB, with any of the given species.
Resolve the given Mention to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.
Resolve the given Mention to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB. If the mention is not found, use the given text transforming functions to create and lookup alternate keys.
Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.
Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB. If the text is not found, use the given text transforming functions to create and lookup alternate keys.
Resolve the given Mention to an optional entry in a knowledge base, failing if the entry is not for humans.
Resolve the given Mention to an optional entry in a knowledge base, failing if the entry is not for humans. Return a resolution for a human entry, if any found.
Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans.
Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans. Return a resolution for a human entry, if any found.
Resolve the given Mention to an optional entry in a knowledge base, failing if the entry is not for humans.
Resolve the given Mention to an optional entry in a knowledge base, failing if the entry is not for humans. If the mention is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for a human entry, if any found.
Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans.
Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans. If the text is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for a human entry, if any found.
Resolve the given Mention to an optional entry in a knowledge base which explicitly does not have an associated species.
Resolve the given Mention to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. Return a resolution for the entry, if any found.
Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species.
Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. Return a resolution for the entry, if any found.
Resolve the given Mention to an optional entry in a knowledge base which explicitly does not have an associated species.
Resolve the given Mention to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. If the mention is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.
Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species.
Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. If the text is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.
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.
Class implementing alternate key mention lookups for cell types which can be inferred from the organ name and specific contextual suffixes. Written by Tom Hicks. 12/20/2015. Last Modified: Fix: call superclass constructor.