Abstract: Systems, methods and articles of manufacture are disclosed for searching chemical compounds referenced in chemical literature. References to chemical compounds in the documents may be transformed to corresponding references using a standard notation for representing chemical compounds. Criteria specifying desired molecular characteristics may be received. A regular expression may be generated based on the received criteria. The chemical documents may be searched using the regular expression. Based on the search, a chemical document may be determined that references a chemical compound satisfying the received criteria. Further, the regular expression may be generated based on the received criteria and a received mutation rule. Based on the generated regular expression and the chemical documents, one or more chemical compounds may be discovered that satisfy both the received criteria and the received mutation rule, but that is are not referenced in the chemical documents.

Abstract: Methods, systems, and articles of manufacture that may be used to create and share annotations for query components, such as query conditions, in an effort to share domain knowledge, are provided. The annotations may be created by users with particular domain knowledge and may contain information useful to other users when building queries including the annotated query components. An annotation may indicate a particular format or syntax for an associated query component. In some cases, a replacement to the associated query component is suggested.

Abstract: An apparatus and method define the concept of a “database breakpoint.” One or more conditions in the database are specified as a database breakpoint in a debug environment for debugging a computer program that accesses the database. When the database conditions exist, one or more debug functions may be performed with respect to the execution of the computer program. Examples of debug functions include halting execution of the computer program and halting operations to the database by other programs. With both the computer program and database halted, the user may then interrogate the database to determine its state, and may interrogate the program to determine its state. Database breakpoints greatly enhance the utility of a debugger by providing additional conditions for debugging a computer program that accesses a database.

Abstract: A method and apparatus, and article of manufacture are provided to process an abstract query of a database abstraction constructed over an underlying physical data storage mechanism. The database may comprise a single data source, or a federated source spanning multiple systems. Embodiments of the invention process an abstract query by generating an intermediate representation of the abstract query. In one embodiment, the intermediate representation comprises an abstract query plan. An abstract query plan includes a combination of elements from the data abstraction model and elements relating to the underlying physical data storage mechanism. Once generated, a back-end component may easily traverse the abstract query plan to generate an SQL statement (or other resolved query) corresponding to the abstract query.

Abstract: Embodiments of the invention relate data retrieved from the logical fields of an abstract database using a timeline. The logical fields specified by a database abstraction model are extended to include attributes that specify where data corresponding to a logical field occurs on a timeline. Query results may be displayed by ordering query results as points (for an event) or segments (for a duration) on the timeline. Further, query processing techniques disclosed by the present invention allow users to include temporal operators such as “before,” “after,” “during,” and “within” in an abstract query. Temporal operators provide users with the ability to include temporal relationships in an abstract query, without having to construct a complex conditional expression from more primitive logical operators (e.g., “ands” and “ors”).

Abstract: The present invention is generally directed to a system, method and article of manufacture for accessing data represented abstractly through an abstraction model. In one embodiment, a data repository abstraction layer provides a logical view of an underlying data repository that is independent of the particular manner of data representation. For each successive query, the data repository abstraction layer is replaced or redefined to provide a restricted logical view of the underlying data repository.

Abstract: The present invention is generally directed to a system, method and article of manufacture for accessing data represented abstractly through an abstraction model. In one embodiment, a data repository abstraction layer provides a logical view of an underlying data repository that is independent of the particular manner of data representation. For each successive query, the data repository abstraction layer is replaced or redefined to provide a restricted logical view of the underlying data repository.

Abstract: The present invention is generally directed to a system, method and article of manufacture for accessing data represented abstractly through an abstraction model. In one embodiment, a data repository abstraction layer provides a logical view of an underlying data repository that is independent of the particular manner of data representation. For each successive query, the data repository abstraction layer is replaced or redefined to provide a restricted logical view of the underlying data repository.

Abstract: Embodiments of the invention provide methods, systems and articles of manufacture for transforming a physical query (e.g., written in SQL) into an abstract query than can be run against an abstract database described by a database abstraction model. In one embodiment, the transformation occurs as a multiple step process: first, transformation of the physical query into an intermediate representation, such as an abstract query plan, and second, transformation of the intermediate representation into an abstract query. There are thousands upon thousands of existing physical (e.g., SQL) queries. Rather than just abandon these existing queries in favor of an abstract database, embodiments of the present invention provide for reverse query processing, that is, for creating an abstract query of the abstract database from a physical query (e.g., an SQL query) of the physical database underlying the abstraction.

Abstract: A method, system and article of manufacture for managing metadata associated with a data abstraction model abstractly describing data in a database. One embodiment provides a method of managing metadata describing objects of a data abstraction model with logical fields that define abstract views of physical data in a database. The method comprises traversing a logical tree structure representing the data abstraction model. The logical tree structure has a plurality of nodes, each representing a logical field or a category of logical fields of the data abstraction model. The method further comprises identifying metadata describing logical fields or categories represented by the plurality of nodes. The identified metadata is stored in a queryable database. A user is allowed to query the database to identify objects in the data abstraction model that may be used to construct an abstract query.

Abstract: An apparatus, program product and method dynamically optimize prepared statements resident in a statement pool to permit subsequent reuses of such statements to utilize the optimized representations of such statements. The optimization of pooled statements may be performed responsive to the tracked usage of the statements in a statement pool, to direct the overhead associated with such optimization to those statements that are more likely to be utilized in the future. Among a multitude of possible optimizations, a pooled statement that requests data in a format other than that utilized by the database being accessed may be modified to request the data in the format used by the database, thereby decreasing the overhead in the database associated with format conversions.

Abstract: An apparatus, program product and method dynamically optimize prepared statements resident in a statement pool to permit subsequent reuses of such statements to utilize the optimized representations of such statements. The optimization of pooled statements may be performed responsive to the tracked usage of the statements in a statement pool, to direct the overhead associated with such optimization to those statements that are more likely to be utilized in the future. Among a multitude of possible optimizations, a pooled statement that requests data in a format other than that utilized by the database being accessed may be modified to request the data in the format used by the database, thereby decreasing the overhead in the database associated with format conversions.

Abstract: An apparatus, program product and method dynamically optimize prepared statements resident in a statement pool to permit subsequent reuses of such statements to utilize the optimized representations of such statements. The optimization of pooled statements may be performed responsive to the tracked usage of the statements in a statement pool, to direct the overhead associated with such optimization to those statements that are more likely to be utilized in the future. Among a multitude of possible optimizations, a pooled statement that requests data in a format other than that utilized by the database being accessed may be modified to request the data in the format used by the database, thereby decreasing the overhead in the database associated with format conversions.

Abstract: Embodiments are provided for associating a virtual column with a target physical table. The data for the virtual column originates from a source physical table where the data physically resides. In this way, users can access the data in a manner consistent with the users' logical perspective of the data.

Abstract: Methods, systems, and articles of manufacture that allow saved abstract queries to be referenced from within query statements constructed using standard query languages, such as Structured Query Language (SQL), are provided.

Abstract: Embodiments of the present invention provide methods and systems for increasing the flexibility and reusability of parameterized queries. A user may be allowed to select and run a predefined query. If the query is a parameterized query, the user may be prompted to input one or more parameters. Embodiments of the invention allow the user to recommend a parameter that retrieves maximum or minimum results for the query instead of specifying a parameter. In response to such a user selection, a predefined parameter may be inserted as a parameter for the query. Alternatively, the query may be modified by changing or removing one or more query conditions to achieve the desired results.

Abstract: A system, method and article of manufacture for accessing data are disclosed. In general, data access is facilitated by a query configured with a correlation criterion or criteria. The presence of the correlation criteria facilitates the introduction of additional correlation logic to be applied to conditions of the query. In general, correlation criteria are contemplated which support correlation of entities based on time, physical location and age, for example.

Abstract: A method, system and article of manufacture for query processing and, more particularly, for managing execution of a query against data in a database. One embodiment comprises receiving a query having (i) at least one result field configured to return data from at least one data record included with the database, and (ii) a query condition comprising a field and a query object associated with the field by an operator configured to select values for the field from the query object. The method further comprises determining whether the query object is configured to provide one or more valid values for the field. If the query object is not configured to provide one or more valid values for the field, the query object is transformed into a transformed query object that is configured to provide one or more valid values for the field. Then, the query is executed against the database.

Abstract: A method, system and article of manufacture for processing requests in web applications and, more particularly, for processing requests between two different applications. One embodiment provides a computer-implemented method of processing a copy request in a distributed environment including at least a first and a second application. The method comprises receiving, from the first application, a copy request for a copy of a selected object. A fully defined instance of the selected object resides in the second application and only a representation of the fully defined instance resides in the first application. The method further comprises generating, by the second application, an object descriptor representing the fully defined instance. At least a portion of the fully defined instance is excluded in the object descriptor. The object descriptor is transmitted from the second to the first application. Thereby, access by the first application to the fully defined instance is prevented.

Abstract: An apparatus and method modify a saved query based on a change in a query value meaning that changes over time. In preferred embodiments a graphical query interface displays an option to adjust query values of a saved database query. A query adjustment mechanism then adjusts the value of the query to compensate for the change in the meaning of the query value since the query was created such that the adjusted query will have the same basic meaning as when the query was originally created. Preferred Embodiments allow the user to specify to adjust the query to the current date or to a specified date in the past.