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Open Knee(s) project will generate a plethora of heterogeneous data sets, e.g. DICOM images, joint/tissue mechanical testing data, etc. It is unnecessary and sometimes clumsy to put the data into source code repositories. The workflow of the "Downloads" section at the project site also seems cumbersome for intermediate storage of data, which may not be release ready. This specification is targeted to find a solution for online storage of data (in-house or at Open Knee(s) project site) that will accommodate the workflow of data collection, analysis, and public release. A separate project site at SimTK.org is available to expand management of data and relevant information for biomechanics studies beyond the realm of Open Knee(s), see https://simtk.org/home/dmmb. Open Knee(s) project will generate a plethora of heterogeneous data sets, e.g. DICOM images, joint/tissue mechanical testing data, etc. It is unnecessary and sometimes clumsy to put the data into source code repositories. The workflow of the "Downloads" section at the project site also seems cumbersome for intermediate storage of data, which may not be release ready. This specification is targeted to find a solution for online curation and storage of data (in-house or at Open Knee(s) project site) that will accommodate the workflow of data collection, analysis, and public release. A separate project site at SimTK.org is available to expand management of data and relevant information for biomechanics studies beyond the realm of Open Knee(s), see https://simtk.org/home/dmmb.
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Storage of data for future discoverability, retrieval, and dissemination Curation and storage of specimen/sample associated data for discoverability, retrieval, and dissemination
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 * A data management system, e.g. [http://www.midasplatform.org/ Midas Platform]. == Infrastructure ==

 * A data management system, e.g. [http://www.midasplatform.org/ Midas Platform], for data curation.
 * A dissemination platform, e.g. Downloads section of [https://simtk.org/home/openknee], also see ["Infrastructure/Collaboration"]
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 * ["Specifications/Specimens"]
 * ["Specifications/SpecimenPreparation"]

== Related Protocols ==
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== Input == == Specimen/Sample Labeling ==
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== Procedures == === Joint ===
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-- ["aerdemir"] [[DateTime(2014-02-11T13:05:40Z)]] This section may list general purpose procedures and alternatives to utilize the same input to reach the same output. Procedures optimized for specific experimentation protocols should also be provided in here. === Tissue ===
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== Output == 1. Expected samples:

  * Cartilage
   * Test type: Confined compression
   * Sample location:
     * Femur, medial
     * Femur, lateral
     * Tibia, medial
     * Tibia, lateral
     * Patella
  * Meniscus
   * Test type: Confined compression, Uniaxial tension
   * Sample location:
     * medial
     * lateral
  * Ligaments (Anetrior and posterior cruciate ligaments, medial and lateral collateral ligaments, and patellar ligament)
    * Test type: Uniaxial tension
    * Sample location: Mid-substance
  * Tendon (Quadricep)
    * Test type: Uniaxial tension
    * Sample location: Mid-substance

2. Minimum number of samples: 16

  * Compression: 8 (1 patella, 1 trochlear groove, 4 cartilage, 2 meniscus)
  * Tension: 8 (5 ligaments, 2 meniscus, 1 tendon)

 
3. Tissue Sample/data labels:

'''Note:''' Trial number will appear only for data files.


Labeling convention: specimen identifier - tissue type identifier - location identifier (1 character for each direction. e.g MA= medial anterior) - trial number/ sample number identifier

 * Cartilage:
  * OK_ _-FMC-MXXX-_ _ (medial femoral cartilage)
  * OK_ _-FMC-LXXX-_ _ (lateral femoral cartilage)
  * OK_ _-FMC-AXXX-_ _ (Trochlear groove)
  * OK_ _-PTC-MXXX-_ _ (Patellar cartilage)
  * OK_ _-TBC-MXXX-_ _(medial tibial cartilage)
  * OK_ _-TBC-LXXX-_ _(lateral tibial cartilage)


'''Note:''' Depth identifiers: u = superficial layer, v=middle layer, w=deep layer

 * Meniscus:
  * OK_ _-MNS-(MAXX/MPXX/MCXX)-_ _ (Location identifiers : A (anterior), P (posterior), C (center))
  * OK_ _-MNS-(LAXX/LPXX/LCXX)-_ _


 * Tendon:
  * OK_ _-QAT-(SXXX/CXXX/IXXX)-_ _ (Location identifiers : S (Superior), C (center/ mid-substance), I (Inferior))

 * Ligaments:
  * OK_ _-ACL-(SXXX/CXXX/IXXX)-_ _ (Location identifiers : S (Superior), C (center/mid-substance), I (Inferior))
  * OK_ _-PCL-(SXXX/CXXX/IXXX)-_ _
  * OK_ _-MCL-(SXXX/CXXX/IXXX)-_ _
  * OK_ _-LCL-(SXXX/CXXX/IXXX)-_ _
  * OK_ _-PTL-(SXXX/CXXX/IXXX)-_ _

attachment:t_loc-labels.png

 attachment:tissue_label.txt

== Data Labeling ==
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== Data Curation ==

== Data Dissemination ==

TableOfContents()

Overview

Open Knee(s) project will generate a plethora of heterogeneous data sets, e.g. DICOM images, joint/tissue mechanical testing data, etc. It is unnecessary and sometimes clumsy to put the data into source code repositories. The workflow of the "Downloads" section at the project site also seems cumbersome for intermediate storage of data, which may not be release ready. This specification is targeted to find a solution for online curation and storage of data (in-house or at Open Knee(s) project site) that will accommodate the workflow of data collection, analysis, and public release. A separate project site at SimTK.org is available to expand management of data and relevant information for biomechanics studies beyond the realm of Open Knee(s), see https://simtk.org/home/dmmb.

Target Outcome

Curation and storage of specimen/sample associated data for discoverability, retrieval, and dissemination

Prerequisites

Infrastructure

Previous Protocols

  • ["Specifications/Specimens"]
  • ["Specifications/SpecimenPreparation"]

Any experimentation protocol, see

  • ["Specifications/ExperimentationAnatomicalImaging"]
  • ["Specifications/ExperimentationJointMechanics"]
  • ["Specifications/ExperimentationTissueMechanics"]

Protocols

Specimen/Sample Labeling

Joint

Tissue

1. Expected samples:

  • Cartilage
    • Test type: Confined compression
    • Sample location:
      • Femur, medial
      • Femur, lateral
      • Tibia, medial
      • Tibia, lateral
      • Patella
  • Meniscus
    • Test type: Confined compression, Uniaxial tension
    • Sample location:
      • medial
      • lateral
  • Ligaments (Anetrior and posterior cruciate ligaments, medial and lateral collateral ligaments, and patellar ligament)
    • Test type: Uniaxial tension
    • Sample location: Mid-substance
  • Tendon (Quadricep)
    • Test type: Uniaxial tension
    • Sample location: Mid-substance

2. Minimum number of samples: 16

  • Compression: 8 (1 patella, 1 trochlear groove, 4 cartilage, 2 meniscus)
  • Tension: 8 (5 ligaments, 2 meniscus, 1 tendon)

3. Tissue Sample/data labels:

Note: Trial number will appear only for data files.

Labeling convention: specimen identifier - tissue type identifier - location identifier (1 character for each direction. e.g MA= medial anterior) - trial number/ sample number identifier

  • Cartilage:
    • OK_ _-FMC-MXXX-_ _ (medial femoral cartilage)
    • OK_ _-FMC-LXXX-_ _ (lateral femoral cartilage)
    • OK_ _-FMC-AXXX-_ _ (Trochlear groove)
    • OK_ _-PTC-MXXX-_ _ (Patellar cartilage)
    • OK_ _-TBC-MXXX-_ _(medial tibial cartilage)
    • OK_ _-TBC-LXXX-_ _(lateral tibial cartilage)

Note: Depth identifiers: u = superficial layer, v=middle layer, w=deep layer

  • Meniscus:
    • OK_ _-MNS-(MAXX/MPXX/MCXX)-_ _ (Location identifiers : A (anterior), P (posterior), C (center))
    • OK_ _-MNS-(LAXX/LPXX/LCXX)-_ _
  • Tendon:
    • OK_ _-QAT-(SXXX/CXXX/IXXX)-_ _ (Location identifiers : S (Superior), C (center/ mid-substance), I (Inferior))
  • Ligaments:
    • OK_ _-ACL-(SXXX/CXXX/IXXX)-_ _ (Location identifiers : S (Superior), C (center/mid-substance), I (Inferior))
    • OK_ _-PCL-(SXXX/CXXX/IXXX)-_ _
    • OK_ _-MCL-(SXXX/CXXX/IXXX)-_ _
    • OK_ _-LCL-(SXXX/CXXX/IXXX)-_ _
    • OK_ _-PTL-(SXXX/CXXX/IXXX)-_ _

attachment:t_loc-labels.png

  • attachment:tissue_label.txt

Data Labeling

  • Online storage of annotated data for prospective
    • discoverability (for internal use)
    • retrieval (for internal use),
    • and dissemination (through Open Knee(s) site at SimTK.org)

Data Curation

Data Dissemination

Specifications/DataManagement (last edited 2019-04-05 18:29:59 by owings)