24. A system comprising a plurality of computers at least two of which are coupled together through a data communications network, said system comprising: a tokenizer and a token processing module comprised of computer instructions in data storage distributed across the plurality of computers directing the plurality of computers to parse text of each of at least one text document into text tokens and assign semantic meaning to words of the parsed text tokens, where assigning comprises applying a plurality of regular expressions, rules and a set of dictionaries, where the set of dictionaries is selected from the group consisting of: a first collection of dictionaries consisting of a common chemical prefix dictionary and a common chemical suffix dictionary to recognize chemical name fragments and a second collection of dictionaries consisting of the common chemical prefix dictionary, the common chemical suffix dictionary to recognize chemical name fragments and a dictionary of stop words to eliminate erroneous chemical name fragments; the instructions of the token processing module directing the plurality of computers to recognize any substructures present in the chemical name fragments; the instructions of the token processing module directing the plurality of computers to extract keywords from the text document, where the keywords are associated with the recognized chemical name fragments and the substructures and to index the extracted keywords in a text index; the instructions of the token processing module directing the plurality of computers to add each of the recognized chemical name fragments and the substructures that do not contain a number to the text index; the instructions of the token processing module directing the plurality of computers to, for each of the at least one text document, determine structural connectivity information within each of the recognized chemical name fragments and the substructures that do not contain a number; the instructions of the token processing module directing the plurality of computers to index representations of the recognized chemical name fragments and the substructures in association with the determined structural connectivity information into a plurality of chemical connectivity tables of a chemical substructure index, where indexing the representations comprises: in a loop, testing each of the recognized chemical name fragments in the at least one text document to see if the recognized chemical name fragment occurs in a dictionary of SMILES fragments, where if it does then a SMILES expression for the recognized chemical name fragment is added to the chemical substructure index, then determining if the recognized chemical name fragment occurs in a MOL file dictionary, where if it does then a MOL file expression for the fragment token is added to the chemical substructure index, and storing the text index in association with the chemical substructure index; a searcher module comprised of computer instructions distributed across the plurality of computers and a graphical user interface comprised of a display configured to display a graphical list of substructures and a keyboard connected to a computer of the plurality of computers directing the plurality of computers to search the text index and the chemical substructure index, where the search comprises first entering search terms comprising one or more chemical fragment names and then selecting graphical representations of one or more substructures, where the selecting comprises using the graphical user interface as a pointer to the graphical list of substructures; and the graphical user interface configured to receive a search result, where the search result is an intersection of the chemical substructure index and the text index, identifying at least one text document where there are found chemical compounds that contain a reference to the search temis and the one or more substructures and where the search terms are found in the text index.
24. A system comprising a plurality of computers at least two of which are coupled together through a data communications network, said system comprising: a tokenizer and a token processing module comprised of computer instructions in data storage distributed across the plurality of computers directing the plurality of computers to parse text of each of at least one text document into text tokens and assign semantic meaning to words of the parsed text tokens, where assigning comprises applying a plurality of regular expressions, rules and a set of dictionaries, where the set of dictionaries is selected from the group consisting of: a first collection of dictionaries consisting of a common chemical prefix dictionary and a common chemical suffix dictionary to recognize chemical name fragments and a second collection of dictionaries consisting of the common chemical prefix dictionary, the common chemical suffix dictionary to recognize chemical name fragments and a dictionary of stop words to eliminate erroneous chemical name fragments; the instructions of the token processing module directing the plurality of computers to recognize any substructures present in the chemical name fragments; the instructions of the token processing module directing the plurality of computers to extract keywords from the text document, where the keywords are associated with the recognized chemical name fragments and the substructures and to index the extracted keywords in a text index; the instructions of the token processing module directing the plurality of computers to add each of the recognized chemical name fragments and the substructures that do not contain a number to the text index; the instructions of the token processing module directing the plurality of computers to, for each of the at least one text document, determine structural connectivity information within each of the recognized chemical name fragments and the substructures that do not contain a number; the instructions of the token processing module directing the plurality of computers to index representations of the recognized chemical name fragments and the substructures in association with the determined structural connectivity information into a plurality of chemical connectivity tables of a chemical substructure index, where indexing the representations comprises: in a loop, testing each of the recognized chemical name fragments in the at least one text document to see if the recognized chemical name fragment occurs in a dictionary of SMILES fragments, where if it does then a SMILES expression for the recognized chemical name fragment is added to the chemical substructure index, then determining if the recognized chemical name fragment occurs in a MOL file dictionary, where if it does then a MOL file expression for the fragment token is added to the chemical substructure index, and storing the text index in association with the chemical substructure index; a searcher module comprised of computer instructions distributed across the plurality of computers and a graphical user interface comprised of a display configured to display a graphical list of substructures and a keyboard connected to a computer of the plurality of computers directing the plurality of computers to search the text index and the chemical substructure index, where the search comprises first entering search terms comprising one or more chemical fragment names and then selecting graphical representations of one or more substructures, where the selecting comprises using the graphical user interface as a pointer to the graphical list of substructures; and the graphical user interface configured to receive a search result, where the search result is an intersection of the chemical substructure index and the text index, identifying at least one text document where there are found chemical compounds that contain a reference to the search temis and the one or more substructures and where the search terms are found in the text index. 25. The system as in claim 24 , wherein the search further comprises first entering the one or more chemical fragment names and additionally entering at least one keyword, and where the search result is identifying at least one text document where there are found the at least one keyword, the chemical compounds that contain the selected substructures, and the connectivity specified by the one or more chemical fragment names and the selected substructures.