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Entity-Relationship Model of the BeeSpace Navigator Database September 2007

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Entity-Relationship Model of the BeeSpace Navigator Database – September 2007

This is the database scheme for BeeSpace v3. The 3 relational tables at the top are the session dynamic values; they are filled in as the user navigates through the system. The tables left to right store values for the user logins, the user objects (spaces and regions), and the user queries. The 2 relational tables at the bottom are the collection static values, they are filled in as new documents are imported into the system. The left table is the parsed entities from the contents while the right table is the documents with metadata. Adding entities is easy, requiring only an alter table and an add column command.
The Java web application with the user interface also retrieves from other sources besides the MySQL database. The full-text indexing for search is supported by the Lemur/Indri toolkit. Temporary indexes in the local file system, such as the semantic graph for mutual information, are only dynamically generated, not permanently stored.

User Table
The User Table contains the directory of BeeSpace users. It stores both visible and hidden fields of a user's account.

Column definitions:

uid is auto-generated user id (PK)

unique email of user

given name

family name

user's organization


user's state variable

user's secret

User Object Table
The User Object Table stores user objects (e.g. regions/spaces) and their metadata.

Column definitions:

oid is auto-generated object id (PK)

owner of this operation

type code of object

link to object

user-assigned group

user-assigned label

user-assigned description text

object size

last create/update timestamp

is-public flag

uid is of User Object Table

User Query Table
The User Query Table stores user queries, which could be used for displaying or re-executing history of user operations, etc.

Column descriptions:

sid is auto-generated query id (PK)

owner of this operation

op code

first operand

second operand

collection id

last create/update timestamp

oid is of User Query Table

Entity Table
The Entity Table stores entities found from Jing's NER program. Fields offset and length are character based metrics for identifying the entity text. The entity field is rather redundant and was used for backtracing/debugging primarily.

Column definitions:

eid is auto-generated entity record id (PK)

unique email of user

field in record entity is found

character offset into field of start pos

character length of entity text

the actual entity text (mainly for backtracing)

cid is of NER Table

Citation Table
The Citation Table stores the normalized contents of a beespace citation record. Note: the genes field corresponds to human-annotations that come directly from PubMed for Biosis and hence are rather sparse.

Column definitions:

cid is auto-generated citation db id (PK)

citation external docno

title of citation

abstract of citation

publication source of citation

author field of citation

mesh field of citation

chemicals field of citation

keywords field of citation

genes field of citation

publication date

p. of

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