Best practices for Archival Processing of Research Objects (a librarian view)
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Best practices for Archival Processing of Research Objects (a librarian view)

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This slideset describes a set of best practices for archival processing or Research Objects. It is part of the Research Object Knowledge Hub (http://researchobject.org/), which has been created in the ...

This slideset describes a set of best practices for archival processing or Research Objects. It is part of the Research Object Knowledge Hub (http://researchobject.org/), which has been created in the context of the Wf4Ever project (http://www.wf4ever-project.eu/)

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  • Research is increasingly digital. Most of research results are disseminated in the form of electronic papers through traditional communication channels, such as conferences, journals, or using new mediums such as microblogging. While electronic papers have played and continue to play a primordial role in the dissemination of research results, researchers now recognize that they are by no means sufficient to communicate and share information about research investigations. Indeed, the hypothesis investigated during the research, the experiment designed to assess the validity of the hypothesis, the process (workflow) used to ran the experiment, the datasets used and the results produced by the experiment, and the conclusions drawn by the scientist, are all elements that may be needed to understand, assess the claim, or be able to re-use the results of previous research investigations. Research objects are a new abstractionthat aggregate all these elements. Research object provide an entry point to the elements that are necessary or useful to understand and reuse research results. A particular feature of research objects is that they contain workflows that specify and implements data intensive scientific experiments.
  • Workflows are now widely used in modern sciences, notably life sciences, as a means for specifying and enacting scientific experiments. The following slide illustrates an example of a workflow that implements an in silico experiment.The workflow consists of three operations. The IdentifyProtein operation takes as input peptide masses obtained from the digestion of a protein together with an identification error and outputs the accession number of protein with the ``best'' match. Given a protein accession, the operation GetHomologous performs a homology search and returns the list of similar proteins. The accessions of the homologous proteins are then used to feed the execution of the GetGOTerm operation to obtain their corresponding gene ontology term.
  • A Research Object can be also identified by a Uniform Resource Identifier (URI), like the Digital Object Identifier (DOI). In this way, an RO can be shared and cited in scholarly articles or any form of online communications, providing an essential collection of contextual information for re-users, reviewers or collaborators to understand, reuse, validate and reproduce research findings.
  • This figure provides an overview of the RO Model, which includes the following constructs:ResearchObject: Represents an aggregation of resources. It acts as an entry point to the research object.Resource: Represents a resource that can be aggregated within a research object. A resource can be a workflow, web service, document, data item, data set, workflow run, software or a research object. Typically, a Research Object aggregates multiple Resources.Annotation: Used for describing research objects, their aggregated resources, as well as the relationship between resources. Three kinds of elements are used to specify annotations:Annotation: Represents the annotation itself.Target: Used to specify the resource or research object subject to annotation.Body: Comprises a description of the target in the form of a set of RDF statements, which can be specifying the date of creation of the target, or its relationship with other resources or research objects.
  • A special kind of ROs is workflow-centric ROs, which refer to research objects that aggregate workflows, or more specifically workflow templates:A workflow template is a network in which the nodes are processes and the edges represent data links that connect the output of a given process to the input of another process, specifying that the artefacts produced by the former are used to feed the latter.A process is used to describe a class of actions that when enacted give rise to process runs. Processes specify the software component (e.g., web service) responsible for undertaking those actions.
  • Using ORE, a workflow-centric research object is defined as a resource that aggregates other resources, i.e., workflow(s), provenance, other objects and annotations. For ex- ample, the RDF turtle snippet illustrated below specifies that a research object identified by :wro aggregates a workflow template :pathway wf sp, a workflow run :pathway wf run, and an annotation :wfannot.
  • We also use the Annotation Ontology (AO), which provides a common model for annotating resources. This differs from myExperiment packs, which use a vocabulary that is mapped to Open Annotation Collaboration (OAC)910. Several types of annotations are supported by the Annotation Ontology, e.g., comments, textual annotations (classic tags) and semantic annotations which relate elements of the research objects to concepts from underlying domain ontologies.
  • Thero ontology: Provides basic structure for the description of aggregated resources and the annotations that are made on those resources.The roevo ontology: Enables the representation of the different stages of the Research Objects life-cycle, their dependencies, as well as the corresponding versions of Research Objects and their aggregated resources, with the associated changes in these resources.Thewfdescontology: A vocabulary for the description of workflows. It is targeted at providing an abstraction that can be mapped to different particular workflow systems. Thewfprovontology: A vocabulary for the description of provenance information about actual executions of workflows.The RO ontologies contain extension points that allow third parties to customise them in order to define specific kinds of research objects or to describe more detailed information that is specific to their tools and application scenarios.

Best practices for Archival Processing of Research Objects (a librarian view) Best practices for Archival Processing of Research Objects (a librarian view) Presentation Transcript

  • BEST PRACTICES FOR ARCHIVAL PROCESSING OF RESEARCH OBJECTS (A LIBRARIAN VIEW) Sara Pérez (UPM), Oscar Corcho (UPM), Raúl Palma (PSNC), Piotr Holubowicz (PSNC)
  •  This work is licensed under the Creative Commons Attribution 3.0 Unported License You are free: Research Object Knowledge Hub  January 2014 LICENSE to Share — to copy, distribute and transmit the work  to Remix — to adapt the work   Under the following conditions  Attribution — You must attribute the work by inserting   “[source http://researchobject.org/]” at the end of each reused slide a credits slide stating These slides are partially based on “Best practices for archival processing of research objects (a librarian view)” by S. Pérez, O. Corcho, R. Palma, P. Holubowicz http://researchobject.org/ 2
  • Introduction: An overview of Research Objects  Research Object Model  LifeCycle of Research Objects  Storage architecture for ROs  Archival processing of ROs  Conclusions Research Object Knowledge Hub  January 2014 OUTLINE 3 View slide
  • FROM ELECTRONIC PAPERS TO RESEARCH OBJECTS January 2014 Research Object Knowledge Hub Scientists Hypothesis Experiments Research Object Electronic paper Annotations Results Provenance 4 Datasets View slide
  • Example of a scientific workflow that implement a proteomic experiment  The analysis operations that compose the workflow are provided in this case by third party web services. Research Object Knowledge Hub  January 2014 WORKFLOW: EXAMPLE 5
  • A research object aggregates all elements that are necessary to understand research investigations  Methods (experiments) are viewed as first class citizens  Promote reuse  Enable the verification of reproducibility of the results  They can be identified by a URI (like the DOI), so they can be shared and cited. Research Object Knowledge Hub  January 2014 BENEFITS OF RESEARCH OBJECTS 6
  • Introduction: An overview of Research Objects  Research Object Model  LifeCycle of Research Objects  Storage architecture for ROs  Archival processing of ROs  Conclusions Research Object Knowledge Hub  January 2014 OUTLINE 7
  • January 2014 RESEARCH OBJECT MODEL: OVERVIEW Research Object Knowledge Hub 8
  • January 2014 WORKFLOW TEMPLATE AND WORKFLOW RUN Research Object Knowledge Hub 9
  • GROUNDING WORKFLOW-CENTRIC RESEARCH OBJECTS USING SEMANTIC TECHNOLOGIES  Research objects use the Object Exchange and Reuse (ORE) model, to represent aggregation. Research Object Knowledge Hub Workflow-centric research objects are encoded using RDF, according to a set of ontologies that are publicly available January 2014  10
  •  We use the Annotation Ontology (AO), to annotate research object resources and their relationships. January 2014 GROUNDING WORKFLOW-CENTRIC RESEARCH OBJECTS USING SEMANTIC TECHNOLOGIES (CONT.) Research Object Knowledge Hub 11
  •  Research Object Knowledge Hub The Research Object Model provides a number of basic ontologies that are used within this aggregation/annotation framework to describe specifics of the Workflow-centric Research Objects. These are: January 2014 GROUNDING WORKFLOW-CENTRIC RESEARCH OBJECTS USING SEMANTIC TECHNOLOGIES (CONT.) 12
  • Introduction: An overview of Research Objects  Research Object Model  LifeCycle of Research Objects  Storage architecture for ROs  Archival processing of ROs  Conclusions Research Object Knowledge Hub  January 2014 OUTLINE 13
  • LIFECYCLE OF RESEARCH OBJECTS January 2014 Research Object Knowledge Hub 14
  • RESEARCH OBJECTS AS INFORMATION PACKAGES IN OAIS January 2014 Research Object Knowledge Hub 15
  • Introduction: An overview of Research Objects  Research Object Model  LifeCycle of Research Objects  Storage architecture for ROs  Archival processing of ROs  Conclusions Research Object Knowledge Hub  January 2014 OUTLINE 16
  • CONCEPTUAL ARCHIVAL SYSTEM STORAGE ARCHITECTURE FOR ROS January 2014 Research Object Knowledge Hub 17
  • Introduction: An overview of Research Objects  Research Object Model  LifeCycle of Research Objects  Storage architecture for ROs  Archival processing of ROs  Conclusions Research Object Knowledge Hub  January 2014 OUTLINE 18
  • ARCHIVAL PROCESSING OF RESEARCH OBJECTS 2.0 Quality Assurance on SIP (received files) 2.1 Run virus check 2.2 Check the format and link relations 1.2 Add workflow, hypothesis, datasets, wf-runs, etc. 2.3 Run checklist for completeness 1.3 Create/Verify metadata 2.4 Validate naming conventions 1.4 Identify/Approve the file formats 2.5 Verify that workflow runs belong to the wf in the RO 3.1 Checklists/Monitoring activities 3.2 Create a safe copy of RO metadata file 3.3 Replace and format transformation (if necessary) 3.4 Establish fixity value/mechanism 3.5 Create Archival Metadata Record 1.5 Run checklist for completeness 1.6 Submit SIP 1.7 Receive acknowledgement of submitted files 2.6 Validate RO metadata is completed to Archive’s specifications 2.7 Send acknowledgement to RO contributor 3.6 Create AIP and add record to Preservation Repository 4.0 Generate DIP 4.1 Create the Access Copy 4.2 Create access aid derivatives 4.3 Create Catalog Entry 4.4 Add to Digital Collection 4.5 Verify Catalog, and Digital Collection access Research Object Knowledge Hub 1.1 Create an RO 3.0 Generate AIP January 2014 1.0 Ingest/Upload/Su bmit files 4.6 Update Archival Metadata Record 3.7 Create security copy of Preservation Master 19
  • Key questions for the Repository with regard to the Submission process:  How the ROs’ components have to be prepared and packed to be ingested?  How should RO components be named for transfer to the Repository?  How should RO component files be organized for transfer to the Repository?  What RO metadata Producers are required to include?  How will RO be validated for transfer? Research Object Knowledge Hub How is the mechanism to be used by content Producers to create an RO and aggregate resources to it? January 2014  20
  • CREATE A RESEARCH OBJECT January 2014 1) Make a sketch workflow; 2) Use modules; 3) Think about the output; 4) Provide input and output examples; 5) Annotate; 6) Make it executable from outside the local environment; 7) Choose services carefully; 8) Reuse existing workflows; 9) Test and validate; 10) Advertise and Maintain. Research Object Knowledge Hub Scientists will appreciate guidelines and Best Practices for producing high quality ROs. Example: • • • • • • • • • • 21
  • January 2014 Research Object Knowledge Hub 22
  • ANNOTATIONS dct:subject dct:description Institution dct:publisher Country pav:createdAt Author dct:creator Contributor dct:contributor RO snapshot creator roevo:wasSnapshotedBy RO release/archive creator roevo:wasArchivedBy Notes rdfs:comment Keywords roterms:keywords Title dct:title Creation date dct:created Modification date dct:modified Purpose roterms:performsTask Dependencies (e.g., execution environment) dct:requires Subproperties roterms:requiresHardware Research Object Knowledge Hub Description January 2014 Scientific domain roterms:requiresSoftware roterms:requiresDataset License dct:license Citations dct:isReferencedBy Technical contact roterms:technicalContact General documentation cito:isDocumentedBy 23
  • VERIFY METADATA Research Object Knowledge Hub The author of the changes  The date  Evolution information  Automatic relations between resources  January 2014 The basic metadata may be: 24
  • IDENTIFY/APPROVE FOLDER STRUCTURE For instance: Research Object Knowledge Hub - biblio - produced - used - config - scripts - setup - software - web services - datasets - inputs - results - workflows - components - main - nested January 2014 Verify that the SIP conforms to the folder structure required for processing in the Live Repository. 25
  • RUN CHECKLIST FOR COMPLETENESS (OPTIONAL) January 2014 Research Object Knowledge Hub 26
  • SUBMIT SIP          Contributor contact information who submitted the file (e.g. Name, Agency/Institution, email) Description of data files being ingested Date files ingested Number of (data) files ingested Names of the (data) files ingested Size of the collection of files ingested Validity value for the data files Format Access restrictions (default: public record, no restrictions) Submission Agreement identification (if one is established) Research Object Knowledge Hub  January 2014 Administrative metadata that should be recorded as part of the ingest process includes: 27
  • Research Object Knowledge Hub With the completion of the ingest quality assurance tasks, the contributor should receive an acknowledgement whether the submitted data passed or failed the Quality Assurance process, and if failed, suggestions regarding what needs to be corrected to provide an acceptable submission. January 2014 RECEIVE ACKNOWLEDGMENT OF SUBMITTED FILES 28
  • ARCHIVAL PROCESSING OF RESEARCH OBJECTS 2.0 Quality Assurance on SIP (received files) 2.1 Run virus check 2.2 Check the format and link relations 1.2 Add workflow, hypothesis, datasets, wf-runs, etc. 2.3 Run checklist for completeness 1.3 Create/Verify metadata 2.4 Validate naming conventions 1.4 Identify/Approve the file formats 2.5 Verify that workflow runs belong to the wf in the RO 3.1 Checklists/Monitoring activities 3.2 Create a safe copy of RO metadata file 3.3 Replace and format transformation (if necessary) 3.4 Establish fixity value/mechanism 3.5 Create Archival Metadata Record 1.5 Run checklist for completeness 1.6 Submit SIP 1.7 Receive acknowledgement of submitted files 2.6 Validate RO metadata is completed to Archive’s specifications 2.7 Send acknowledgement to RO contributor 3.6 Create AIP and add record to Preservation Repository 4.0 Generate DIP 4.1 Create the Access Copy 4.2 Create access aid derivatives 4.3 Create Catalog Entry 4.4 Add to Digital Collection 4.5 Verify Catalog, and Digital Collection access Research Object Knowledge Hub 1.1 Create an RO 3.0 Generate AIP January 2014 1.0 Ingest/Upload/Su bmit files 4.6 Update Archival Metadata Record 3.7 Create security copy of Preservation Master 29
  • How to handle received ROs that are not named according to Repository submission guidelines?  How to handle received ROs that are not organized based on Repository submission guidelines?  What quality features of an RO must be validate / evaluate and how?  How will archives validate / evaluate the completeness of the RO metadata?  How will the Repository deal with missing metadata?  What security measures are taken to ensure the safety of the submission and the submitted data before their storage in the Preservation Repository? Research Object Knowledge Hub  January 2014 Key questions for the Repository with regard to the Quality Assurance process: 30
  • Firstly, to ensure that the files are clean and free from viruses, complete a virus check on the submitted files. When infected files are identified, they will need to be logged and the contributor notified for some sort of remediation. Verify that all files have been received, optimally against the manifest that was created when the files were packaged; verify that there are no extra files added to the package, and that the files have arrived intact and unaltered through the transfer process RUN CHECKLIST FOR COMPLETENESS Research Object Knowledge Hub CHECK THE FORMAT AND LINK RELATIONS January 2014 RUN VIRUS CHECK There should be a service/function for testing completeness, executability, repeatability and other desired quality features of a Research Object. 31
  • VALIDATE RO METADATA It would be convenient to identify a subset of required metadata elements that serve as a common guideline for all RO infrastructure developers (descriptive, technical and administrative metadata). Research Object Knowledge Hub The Wf4Ever team also recommends filing naming conventions for the ROs and their resources (data sources/workflow names/ID names, etc.). The Repository will need to define as part of its submission policies the actions it will take when received ROs do not conform to the naming and/or organizational guidelines. January 2014 VALIDATE NAMING CONVENTIONS AND FOLDER STRUCTURE SEND ACKNOWLEDGEMENT An acknowledgement should be sent to the RO contributor notifying her whether the submitted data passed or failed the Quality Assurance process, and if failed, suggestions regarding what needs to be corrected to provide an acceptable submission. 32
  • ARCHIVAL PROCESSING OF RESEARCH OBJECTS 2.0 Quality Assurance on SIP (received files) 2.1 Run virus check 1.1 Create an RO 1.2 Add workflow, hypothesis, datasets, wf-runs, etc. 2.3 Run checklist for completeness 1.3 Create/Verify metadata 2.4 Validate naming conventions 1.4 Identify/Approve the file formats 2.5 Verify that workflow runs belong to the wf in the RO 3.1 Checklists/Monitoring activities 3.2 Create a safe copy of RO metadata file 3.3 Replace and format transformation (if necessary) 3.4 Establish fixity value/mechanism 3.5 Create Archival Metadata Record 1.5 Run checklist for completeness 1.6 Submit SIP 1.7 Receive acknowledgement of submitted files 2.6 Validate RO metadata is completed to Archive’s specifications 2.7 Send acknowledgement to RO contributor 3.6 Create AIP and add record to Preservation Repository 4.0 Generate DIP 4.1 Create the Access Copy 4.2 Create access aid derivatives 4.3 Create Catalog Entry 4.4 Add to Digital Collection 4.5 Verify Catalog, and Digital Collection access 4.6 Update Archival Metadata Record Research Object Knowledge Hub 2.2 Check the format and link relations 3.0 Generate AIP January 2014 1.0 Ingest/Upload/Su bmit files 3.7 Create security copy of Preservation Master 33
  • Key questions for the Repository with regard to the Generate AIP process:           Research Object Knowledge Hub  What are the mappings between expected submitted formats and their companion Preservation Master formats? What tools and processes will be employed to transform an RO component received in one format to another format to produce the Preservation Master? What tools, techniques, or strategies will the Repository employ to populate the missing technical fields? What method will the Repository use to compute, store, re-compute, and compare fixity values for both the Preservation Master and Preservation Master Security Copy(ies)? How would someone perform an audit check to view and/or validate that a file’s integrity is intact? What metadata elements comprise the archival metadata record? / What metadata, (if any), are being created by the archive for inclusion in the AIP and DIP? Will the Repository use a special packaging mechanism (e.g. METS)? Who will have access to the Archival Information Packages? What type of access (read, write)? What will the mechanism(s) to create a security copy(ies), and on what type of media format(s) will the security copy(ies) be stored? What is the mechanism and frequency that the security copy(ies) will be validated? What is the process for restoring the Preservation Master in the event that it is lost or corrupted? What is the process for restoring a Security Copy in the event that it is lost or corrupted? January 2014  34
  • One of the most important aspects to be monitored is the stability of the resources. January 2014 MONITORING AND NOTIFICATION ACTIVITIES Research Object Knowledge Hub 35
  • It is recommended to create a safe copy of the metadata file (manifest.rdf), which is embedded within the RO. Research Object Knowledge Hub REPLACE AND FORMAT TRANSFORMATION (IF NECESSARY) January 2014 CREATE A SAFE COPY OF RO METADATA FILE 36
  • The Preservation Repository should offer checksums checking (at file level). This function will provide a means to verify the bit-level integrity of files managed by this storage. In brief, we recommend that the template should comprise:  Unique ID  Fixity info  Format  Extract RO metadata  Created descriptive metadata  Created technical metadata  Created administrative metadata Research Object Knowledge Hub CREATE ARCHIVAL METADATA RECORD January 2014 ESTABLISH FIXITY VALUE/MECHANISM 37
  • CREATE SECURITY COPY OF THE AIP Security copies of the AIP record should be created and retained. In the event that the AIP is corrupted or lost, it may be recovered from a security copy. Research Object Knowledge Hub What constitutes the Archival “Record” will be defined by each Repository. However, at a minimum, it should include the original (and reformatted, if applicable) RO including the original collection of data files and the originally received RO metadata file. January 2014 CREATE AIP AND ADD RECORD TO PRESERVATION REPOSITORY 38
  • ARCHIVAL PROCESSING OF RESEARCH OBJECTS 2.0 Quality Assurance on SIP (received files) 2.1 Run virus check 1.1 Create an RO 1.2 Add workflow, hypothesis, datasets, wf-runs, etc. 2.3 Run checklist for completeness 1.3 Create/Verify metadata 2.4 Validate naming conventions 1.4 Identify/Approve the file formats 2.5 Verify that workflow runs belong to the wf in the RO 3.1 Checklists/Monitoring activities 3.2 Create a safe copy of RO metadata file 3.3 Replace and format transformation (if necessary) 3.4 Establish fixity value/mechanism 3.5 Create Archival Metadata Record 1.5 Run checklist for completeness 1.6 Submit SIP 1.7 Receive acknowledgement of submitted files 2.6 Validate RO metadata is completed to Archive’s specifications 2.7 Send acknowledgement to RO contributor 3.6 Create AIP and add record to Preservation Repository 4.0 Generate DIP 4.1 Create the Access Copy 4.2 Create access aid derivatives 4.3 Create Catalog Entry 4.4 Add to Digital Collection 4.5 Verify Catalog, and Digital Collection access Research Object Knowledge Hub 2.2 Check the format and link relations 3.0 Generate AIP January 2014 1.0 Ingest/Upload/Su bmit files 4.6 Update Archival Metadata Record 3.7 Create security copy of Preservation Master 39
  • Key questions for the Repository with regard to the Generate DIP process: January 2014 Research Object Knowledge Hub What format will be used for the Access Copy? Same format at Preservation Master? An alternate, compressed format?  What tool(s) are necessary to create the Access/Use Copy?  What access derivatives seem appropriate for your ROs?  What tools do you need to produce these derivatives?  How will ROs be arranged / organized within your archival collection? What constitutes a Collection?  Will individual ROs be entered into your Repository Catalog? If not, how will users find out about the individual ROs? If yes, how will the ROs be entered into your Repository Catalog?  What type of finding aid will you create to describe your RO datasets?  What technology platform and software will be the basis for your RO digital collection?  How will RO be added to the digital collection?  What metadata is necessary to describe and/or manage the RO record in the digital collection?  How will the RO be organized and arranged/categorized in your digital collection?  How will users search and access ROs from your digital collection?  How will the ROs be presented to your users through the digital collection interface?  What test cases will you use to validate the access to your newly added RO?  40
  • Minimum access metadata recommended: URI; Creator; Date; Size; Number of annotations; Relations (was output from; etc.) Some potential access derivatives: • Create HTML version of the Repository’s customized RO metadata file. • Create a zip file containing all of the files in the RO. Research Object Knowledge Hub CREATE ACCESS AID DERIVATIVES January 2014 CREATE THE ACCESS COPY 41
  • Some key points that we recommend offering the user through the search interface: Different views of the RO structure A visualization of the evolution of a research object  A panel showing annotations related to the currently selected resource  Research Object Knowledge Hub  January 2014 ADD TO DIGITAL COLLECTION 42
  • UPDATE ARCHIVAL METADATA RECORD The archival metadata may be updated with metadata regarding the use of resources (information on user registration and possible annotations made by users respect to the resource) and the derivative resources produced during the DIP generation. Research Object Knowledge Hub After the RO entries and/or datasets have been added to the access systems, they should be tested to verify that they are accessible. This can be as simple as navigating through the catalog interface, issuing some test searches, and verifying that the new items are returned in the search results lists. In the case that the research objects are being made available online, the dataset display interface and dataset download mechanisms should also be tested to verify that the research objects can be downloaded. January 2014 VERIFY CATALOG AND DIGITAL COLLECTION ACCESS 43
  • Introduction: An overview of Research Objects  Research Object Model  LifeCycle of Research Objects  Storage architecture for ROs  Archival processing of ROs  Conclusions Research Object Knowledge Hub  January 2014 OUTLINE 44
  • Research object-infrastructure design decisions should include these considerations in terms of functionality and policy: Modular system implementation (support flexible maintenance, extension, integration and interoperability).  Native RO support. It should be implemented alongside the RO model.  Implementation of well-defined and well-documented interfaces (suitable basis of interoperability).  Well-defined migration plans to perform a batch update of resources from one format to another, if necessary. Research Object Knowledge Hub  January 2014 CONCLUSIONS 45
  • Research Object Vocabularies and Ontologies Primer is available at http://wf4ever.github.com/ro-primer/ Research Object Knowledge Hub Research Object Specification is available at http://wf4ever.github.com/ro/ January 2014 RESEARCH OBJECT SPECIFICATIONS ARE PUBLICLY AVAILABLE 46