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Identifiers In Kepler
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- To help scientists manage and share data sets, workflows, and workflow
- computation steps (i.e., actors) as well as semantic descriptions (i.e.,
- metadata and ontology-based annotations) of each of these, we propose
- adding a new file-management middleware subsystem to Kepler.
-
- The main goals of the file-management subsystem are listed below. In
- particular, the subsystem should provide the infrastructure for
- enabling scientists to:
-
- * Search for all known items of interest, including actors, workflows,
- and data sets.
- * Easily organize actors, workflows, and data sets of interest using the
- file-directory metaphor (called "actor libraries" in Ptolemy). For
- example, by allowing a scientist to create and persist a personal
- library, and to browse and search that library. Allow items to be
- organized into multiple local actor libraries, and in multiple
- locations within a library.
- * Persist actors, workflows, and data sets in a network-accesible
- repository (i.e., in the EcoGrid).
- * Retrieve new actors, workflows, and data sets from a network-accessible
- repository (from the EcoGrid) and update changes to existing items.
- * Track both revisions of actors, workflows, and data sets as well as new
- versions (off-shoots or branches) of an item.
- * Store semantic annotations of actors, workflows, and data sets and
- publish those annotations to a network repository (the
- EcoGrid). Retrieve annotations from the network repository.
-
-
- The figure below outlines the architectural components of the
- subsystem. The subsystem assumes the use of [Life-Sciences Identifiers|http://www.i3c.org/wgr/ta/resources/lsid/docs/index.asp]
- (LSIDs) as logical identifiers for actors, workflows, data sets, and
- annotations (and possibly for local "libraries"?). Thus, particular
- files (representing actors, workflows, data sets, or annotations) are
- assigned LSIDs and are accessed via LSIDs.
+ To help scientists manage and share data sets, workflows, and workflow computation steps (i.e., actors) as well as semantic descriptions (i.e., metadata and ontology-based annotations) of each of these, we propose adding a new file-management middleware subsystem to Kepler.
At line 37 added 11 lines.
+ The main goals of the file-management subsystem are listed below. In particular, the subsystem should provide the infrastructure for enabling scientists to:
+
+ * Search for all known items of interest, including actors, workflows, and data sets.
+ * Easily organize actors, workflows, and data sets of interest using the file-directory metaphor (called "actor libraries" in Ptolemy). For example, by allowing a scientist to create and persist a personal library, and to browse and search that library. Allow items to be organized into multiple local actor libraries, and in multiple locations within a library.
+ * Persist actors, workflows, and data sets in a network-accesible repository (i.e., in the EcoGrid).
+ * Retrieve new actors, workflows, and data sets from a network-accessible repository (from the EcoGrid) and update changes to existing items.
+ * Track both revisions of actors, workflows, and data sets as well as new versions (off-shoots or branches) of an item.
+ * Store semantic annotations of actors, workflows, and data sets and publish those annotations to a network repository (the EcoGrid). Retrieve annotations from the network repository.
+
+ The figure below outlines the architectural components of the subsystem. The subsystem assumes the use of [Life-Sciences Identifiers|http://www.i3c.org/wgr/ta/resources/lsid/docs/index.asp] (LSIDs) as logical identifiers for actors, workflows, data sets, and annotations (and possibly for local "libraries"?). Thus, particular files (representing actors, workflows, data sets, or annotations) are assigned LSIDs and are accessed via LSIDs.
+
Lines 42-68 were replaced by lines 20-30
- The main components provide operations over a local data store of
- files. The remote manager provides the operations required to interact
- with the EcoGrid. It also may provide a local cache for
- performance. The LSID manager is used to assign unique identifiers for
- items, e.g., serving as logical identifiers for actors, workflows,
- data sets, and semantic annotations. The logical/physical index
- manager provides operations to related physical files to LSIDs, and to
- access files based on LSIDs. The directory/view manager provides
- operations for local organizations of items into libraries.
-
- The following are a set of possible supported operations (note that
- these are half-baked, if that):
-
- * {{Retrieve(ID)}}. Given an id, the subsystem returns the files
- associated with the item.
- * {{LocalIDs(IDMetadata)}}. Retrieve a list of local LSIDs, based on LSID
- metadata.
- * {{RemoteIDs(IDMetadata)}}. Retrieve a list of remote LSIDs, based on LSID
- metadata.
- * {{Store(ItemHandle, IDMetadata)}}. Construct an LSID with the given
- metadata for the item, and store the item in the local repository.
- * {{GetRemoteUpdates()}}. Retrieve a list of new or updated LSIDs from a remote
- source.
- * {{Update(LSID)}}. Update the given LSID item from a remote source. This
- retrieves a new revision if one exists.
- * {{Branch(LSID)}}. Create a new version of an item. This creates and
- returns a new LSID for the item.
+ The main components provide operations over a local data store of files. The remote manager provides the operations required to interact with the EcoGrid. It also may provide a local cache for performance. The LSID manager is used to assign unique identifiers for items, e.g., serving as logical identifiers for actors, workflows, data sets, and semantic annotations. The logical/physical index manager provides operations to related physical files to LSIDs, and to access files based on LSIDs. The directory/view manager provides operations for local organizations of items into libraries.
+
+ The following are a set of possible supported operations (note that these are half-baked, if that):
+
+ * {{Retrieve(ID)}}. Given an id, the subsystem returns the files associated with the item.
+ * {{LocalIDs(IDMetadata)}}. Retrieve a list of local LSIDs, based on LSID metadata.
+ * {{RemoteIDs(IDMetadata)}}. Retrieve a list of remote LSIDs, based on LSID metadata.
+ * {{Store(ItemHandle, IDMetadata)}}. Construct an LSID with the given metadata for the item, and store the item in the local repository.
+ * {{GetRemoteUpdates()}}. Retrieve a list of new or updated LSIDs from a remote source.
+ * {{Update(LSID)}}. Update the given LSID item from a remote source. This retrieves a new revision if one exists.
+ * {{Branch(LSID)}}. Create a new version of an item. This creates and returns a new LSID for the item.

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This material is based upon work supported by the National Science Foundation under award 0225676. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).

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Long Term Ecological Research Network, UNM National Center for Ecological Analysis and Synthesis, UCSB Biodiversity Research Center, KU San Diego Supercomputer Center, UCSD
 
Arizona State University Napier University University of North Carolina University of Vermont
 
UC Davis Genome Center

Copyright 2004 Partnership for Biodiversity Informatics, University of New Mexico, The Regents of the University of California, and University of Kansas