1. A system for collaborating research, comprising:
a central data processor having a search module for searching data, the central data processor further comprising:
an entity extraction module configured to extract entities from the data;
a network extraction module configured to extract relationships between the extracted entities from the data; and
a formatting module for formatting the extracted entities and the extracted relationships into a visualization format; and
at least one host computer having a user interface for communicating with the central data processor, the user interface comprising:
search tools for allowing a first user of one of the plurality of host computers to communicate a search request to the central data processor, the search request instructing the central data processor to search the data;
selection tools for allowing the first user to select a subset of the data returned by the central data processor in response to the search request, and to initiate the communication of the selected subset of data to the entity extraction module and the network extraction module for data processing;
at least one visualization tool for allowing the first user’s host computer to graphically render the visualization format, and
a collaboration tool input for allowing the first user to give access to the extracted entities and relationships and the visualization format to at least one additional remote user of the plurality of host computers.
2. The system of claim 1, wherein the central data processor further comprises a temporal analysis module configured to extract time information from the data.
3. The system of claim 2, wherein the user interface further comprises a temporal analysis input tool for allowing the first user to initiate the communication of a subset of the data to the temporal analysis module on the central data processor.
4. The system of claim 1, wherein the visualization format is an entity network map where at least one of the extracted entities are shown linked to at least one other extracted entity via at least one of the extracted relationships.
5. The system of claim 1, wherein each respective user interface further comprises a scenario building input tool for creating a system model that includes a set of factors, the factors being derived from the extracted entities and relationships.
6. The system of claim 5, wherein the system model further comprises an influence relationship having a direction and a magnitude of influence exerted by a first factor onto a second factor.
7. The system of claim 6, wherein the magnitude and direction of the influence relationship is determined by any user of the plurality of host computers.
8. The system of claim 6, wherein the magnitude and direction of the influence relationship is determined by the central data processor using the extracted relationships.
9. The system of claim 6, wherein at least one factor has an influence relationship magnitude and direction for every other factor connected to it via an extracted relationship.
10. The system of claim 6, wherein a plurality of factors are graphically located on an influencerinfluenced map according to a calculated value of the magnitudes and directions of every influence relationship associated with each of the respective plurality of factors.
11. The system of claim 10, wherein at least one factor comprises at least one option, each option comprising a value indicating the state of the option.
12. The system of claim 11, further comprising a risk model comprising at least one node associated with one of the at least one options, and wherein the assigned value of at least one node in the risk model is determined with reference to the assigned value of the at least one associated option.
13. The system of claim 1, wherein the system is used to collaborate research on the allocation of resources.
14. The system of claim 1, wherein the system is used to collaborate research relating to market evaluations.
15. The system of claim 1, wherein the system is used to collaborate research relating to network management.
16. A process for determining a user-specified scenario, comprising:
searching a collection of data to find data relevant to a scenario;
processing the relevant data to extract entities and relationships between the entities;
setting influence values for a plurality of extracted entities to indicate the amount of influence each of the plurality of extracted entities has on another extracted entity to which an extracted relationship exists;
associating a set of options with the plurality of the extracted entities; and
populating a risk model comprising a plurality of nodes derived from the extracted entities, wherein at least one of the nodes is associated with an option from the set of options, the option including an associated value, the value usable for calculating an option value associated with a higher level node in the risk model.
17. The process of claim 16, further comprising graphically viewing the extracted entities and relationships.
18. The process of claim 16, further comprising updating the influence values and risk model after repeating the searching, processing, setting, associating and populating using a revised collection of data.
19. The process of claim 18, wherein the updating is automatically performed as a result of a macro of operations.
20. The process of claim 19, wherein the macro is manually created by a user.
21. The process of claim 19, wherein the macro is created by recording a user’s operations.
22. The process of claim 16, wherein the selecting extracted entities comprises graphically viewing the extracted entities and relationships.
23. The process of claim 16, wherein the influence values are set manually by a user.
24. The process of claim 16, wherein the influence values are set automatically based on the extracted relationships.
25. The process of claim 16, wherein the processing the relevant data includes extracting time information.
26. The process of claim 17, wherein the graphically viewing includes rendering an entity network map where at least one of the extracted entities are shown linked to at least one other extracted entity via an extracted relationship.
27. The process of claim 26, wherein the extracted relationship is represented by an influence relationship comprising an influence value exerted by a first extracted entity onto a second extracted entity.
28. The process of claim 27, wherein a magnitude and direction of the influence relationship Is determined by a user.
29. The process of claim 27, wherein a magnitude and direction of the influence relationship is determined automatically using the extracted relationships.
30. The process of claim 27, wherein the graphically rendering further comprises graphically locating a plurality of the extracted entities on an influencerinfluenced map according to a summed value of the influence values associated with each of the respective plurality of entities.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A method for obtaining a modified protein or virus with an intact native binding site and decreased antigenicity, which comprises masking with non-immunogenic molecules the protein or the virus surface, except for the protein or the virus binding site.
2. The method of claim 1, wherein said non-immunogenic molecules are small molecules.
3. The method of claim 2, wherein said non-immunogenic molecules are monosaccharides or fatty acids, or both.
4. The method of claim 3, wherein said monosaccharide is a C3-C6 ketose or aldose.
5. The method of claim 3, wherein said fatty acids are saturated or unsaturated C3-C20 fatty acids.
6. The method of claim 5, wherein said fatty acid is a saturated or unsaturated C3-C20 fatty acid.
7. The method of claim 3, wherein said non-immunogenic molecules are mannose and oleic acid.
8. The method of claim 1, wherein said non-immunogenic molecules are polymers or a polysaccharide.
9. The method of claim 1, wherein molecules which target specific cells or tissues such as cancerous cells or tissues, are chemically attached to functional groups of said non-immunogenic molecules.
10. The method of claim 1, wherein said modified protein is a modified antibody, said method comprising:
(i) attaching an antigen recognized by said antibody to a surface;
(ii) incubating the antibody with said attached antigen, thus forming an antigen-antibody complex;
(iii) masking the antibody surface by chemically attaching non-immunogenic molecules to the antibody surface in the antigen-antibody complex, thus obtaining an antigen-masked antibody complex; and
(iv) separating the masked antibody from the antigen, thus obtaining the desired modified antibody masked with the non-immunogenic molecule, said modified antibody exhibiting an intact native binding site and decreased antigenicity as compared with the unmodified antibody.
11. A modified antibody obtainable by the method of claim 10, said antibody being biologically active, having its native binding site intact and exhibiting decreased immunogenicity as compared with the unmodified antibody.
12. A modified antibody wherein its surface, except for the native binding site, is masked with small molecules covalently linked to functional groups of the antibody molecule, and said small molecules are monosaccharides or fatty acids, or both.
13. The modified antibody of claim 12, wherein said monosaccharide is mannose and said fatty acid is a saturated or unsaturated C3-C20 fatty acid.
14. The modified antibody of claim 11, wherein said antibody is a monoclonal antibody.
15. The modified antibody of claim 11, wherein said antibody is a polyclonal antibody.
16. The modified antibody of claim 11, wherein said antibody is not antigenic within the same or heterologous species.
17. The modified antibody of claim 11, wherein the antibody is an anti-tumor antibody.
18. The method of claim 1, wherein said modified virus is a modified replication-defective virus, said binding site is a native knob binding site, and said method comprises the steps:
(i) incubating the replication-defective virus with an antibody to the knob binding site, thus forming a virus-antibody complex;
(ii) masking the virus surface by chemically attaching non-immunogenic molecules to the virus surface in the virus-antibody complex, thus obtaining a masked virus-antibody complex;
(iii) separating the masked virus from the antibody; and
(iv) removing the residual antibody from the solution by centrifugation,
thus obtaining the desired modified replication-defective virus with an intact native knob binding site and decreased antigenicity as compared with the unmodified virus.
19. A modified replication-defective virus obtainable by the method of claim 18, said virus having a native knob binding site and exhibiting decreased immunogenicity as compared with the unmodified virus.
20. A modified replication-defective virus wherein its surface, except for the native knob binding site, is masked with small molecules covalently linked to functional groups of the virus surface, and said small molecules are monosaccharides or fatty acids, or both.
21. The modified virus of claim 20, wherein said monosaccharide is mannose and said fatty acid is a saturated or unsaturated C3-C20 fatty acid.
22. The modified replication-defective virus of claim 19 selected from an adenovirus, preferably Ad5, a retrovirus, or a recombinant virus which expresses a transgene such as a therapeutic gene for use in gene therapy.
23. A method of claim 1, wherein said modified protein is a modified hormone, said binding site is a receptor binding site, and said method comprises the steps of:
(i) incubating a hormone with its receptor, thus forming a hormone-receptor complex;
(ii) masking the hormone surface by chemically attaching non-immunogenic molecules to the hormone surface in the hormone-receptor complex, thus obtaining a masked hormone-receptor complex; and
(iii) separating the masked hormone from the receptor;
thus obtaining the desired modified masked hormone with an intact receptor binding site and decreased antigenicity as compared with the unmodified hormone.
24. A modified hormone obtainable by the method of claim 23, said hormone having a native hormone binding site and exhibiting decreased immunogenicity as compared to the unmodified hormone.
25. A method of claim 1, wherein said modified protein is a modified enterotoxin, said binding site is a receptor binding site, and said method comprises the steps of:
(i) incubating an enterotoxin with its receptor, thus forming an enterotoxin-receptor complex;
(ii) masking the enterotoxin surface by chemically attaching non-immunogenic molecules to the enterotoxin surface in the enterotoxin-receptor complex, thus obtaining a masked enterotoxin-receptor complex; and
(iii) separating the masked enterotoxin from the receptor; thus obtaining the desired modified masked enterotoxin with an intact receptor binding site and decreased antigenicity as compared with the unmodified enterotoxin.
26. A modified enterotoxin obtainable by the method of claim 25, said enterotoxin having a native hormone binding site and exhibiting decreased immunogenicity as compared to the unmodified enterotoxin.
27. The modified enterotoxin of claim 26, wherein said modified enterotoxin is the enterotoxin of Escherichia coli (LT) or the cholera toxin of Vibrio cholera (CT) with an intact GM1 ganglioside receptor-binding site.
28. The method of claim 4 wherein said monosaccharide is a C5-C6 aldose.
29. The method of claim 28 wherein said C5-C6 aldose is mannose.
30. The method of claim 6, wherein said saturated C3-C20 fatty acid is capric acid, lauric acid, myristic acid, palmitic acid, stearic acid, or arachidic acid, and said unsaturated C3-C20 fatty acid is palmitoleic acid, oleic acid, vaccenic acid, linoleic acid, \u03b3-linolenic acid, linolenic acid, or arachidonic acid.
31. The method of claim 8, wherein said polymer is a hydroxylated polyether and said polysaccharide is dextran, modified dextran, pullulan or mannan.
32. The method of claim 31 wherein said polymer is polyethylene glycol (PEG).
33. The modified antibody of claim 13, wherein said unsaturated C3-C20 fatty acid is oleic acid.
34. The modified virus of claim 21 wherein said unsaturated C3-C20 fatty acid is oleic acid.