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

• 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"]

Previous Protocols

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

Related Protocols

Any experimentation protocol, see

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

Protocols

Specimen/Sample Labeling

Joint

Whole knee specimen labels include the Open Knee(s) abbreviation in lower case, oks, immediately followed by three numerals to indicate specimen number, e.g. 001. An example for knee specimen labeling is in following:

oks001

Open Knee(s) Specimen 1

Tissue

Tissue testing plans of Open Knee(s) will require a large set of tissue samples acquired from a single knee specimen; see details in ["Specifications/SpecimenPreparation"] and ["Specifications/ExperimentationTissueMechanics"]. For example, confined and unconfined compression testing of cartilage will require a total of 10 samples from medial and lateral sides of femur and tibia, and from patella. Compression and tension testing of menisci will require a total of 4 samples from medial and lateral sides. Uniaxial tension testing of ligaments and tendons will require a total of 6 samples from their midsubstance (cruciate, collateral, and patellar ligaments, quadriceps tendon). For a single knee, a total of 20 tissue samples may need to acquired, indicating a need for organization of samples and accompanying data.

Labels for tissue samples include knee specimen label, e.g. oks002, followed by three letter tissue type in upper case, e.g. TBC, four letter tissue location in upper case (from gross to granular location, lower case if at microscale), and two numerals to indicate sample number. When needed, the character X is used as a filler. A few examples for tissue samples are in following:

oks001-PTC-MCXX-02

sample 2 from patellar cartilage of Open Knee(s) Specimen 1, acquired from the medial side at the center.

oks002-MNS-MAvX-01

sample 1 from medial meniscus of Open Knee(s) Specimen 2, acquired from middle layer of the tissue at the anterior side.

Tissue Types

• Bone

  • FMB: femur

  • TBB: tibia

  • FBB: fibula

  • PTB: patella

• Cartilage

  • FMC: femoral cartilage

  • TBC: tibial cartilage

  • PTC: patellar cartilage

• Meniscus

  • MNS: meniscus

• Ligament

  • ACL: anterior cruciate ligament

  • PCL: posterior cruciate ligament

  • MCL: medial collateral ligament

  • LCL: lateral collateral ligament

  • PTL: patellar ligament

• Tendon

  • QAT: quadriceps tendon

Tissue Locations

The tissue location is labeled starting from its gross location and ending with its granular position.

• Bone

  • M or L: medial or lateral

  • A or P: anterior or posterior

  • S or I: superior or inferior

  • C: central

• Cartilage

  • M or L: medial or lateral

  • A or P: anterior or posterior

  • C: central

  • u or v or w: superficial or transitional or deep zone

• Meniscus

  • M or L: medial or lateral

  • A or P: anterior or posterior

  • C: central

  • u or v or w: femur side or mid-substance or tibia side

• Ligament

  • S or I or C: superior or inferior or central

• Tendon

  • S or I or C: superior or inferior or central

Examples (only tissue type and tissue location are shown):

FMC-MAXX

femoral cartilage sample acquired medially and anteriorly

TBC-LAuX

tibial cartilage sample acquired laterally and anteriorly from the superficial zone

FMC-AXXX

femoral cartilage sample acquired from the trochlear groove

MNS-LCwX

sample acquired from lateral meniscus centrally and from mid-substance

MCL-IXXX

medial collateral ligament sample acquired from inferior region

attachment:t_loc-labels.png

Data Labeling

During data collection, the data sets, testing conditions, trials can be labeled through various conventions of experimentation systems and at the convenience of the personnel acquiring the data. Nonetheless, for data curation, organization, and dissemination data labels should be associated with

• specimen/sample label (see above), and
• an indicator/descriptor of experiment condition.

This information can be provided in

• the data label in an abbreviated form, or
• in the header of data files, or
• in a description file associated with the arbitrary data label.

Data Curation

For a given whole knee specimen, Open Knee(s) data will be acquired asynchronously through a variety of modalities including anatomical imaging, mechanical testing of joints, and characterization of tissue specimens, see

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

The in-house data management system, based on [http://www.midasplatform.org/ Midas Platform], will be used as a staging server for data curation and documentation. Once data is collected, the person leading the acquisition activity should ensure association of data labels, specimen/sample labels and provide descriptors of experiment conditions (see section above). In following, data should be uploaded to the in-house data management system for collation of different data sets and for organization. An example hierarchical structure for data organization is in following:

.
├── oks001
│   ├── joint
│   │   ├── patellofemoral
│   │   └── tibiofemoral
│   │       ├── photos
│   │       ├── readme.txt
│   │       └── trial001
│   ├── mri
│   │   ├── cartilage
│   │   ├── connective
│   │   │   ├── axial
│   │   │   ├── coronal
│   │   │   └── sagittal
│   │   └── general
│   ├── photos
│   ├── specs
│   └── tissue
│       ├── bone
│       ├── cartilage
│       ├── ligament
│       │   └── ACL
│       │       ├── photos
│       │       └── readme.txt
│       ├── meniscus
│       └── tendon
├── oks002
├── oks003
├── ...

Data Dissemination

Once data for the whole knee is curated, organized and documented; the project website will be used for dissemination, through the "Downloads" section of https://simtk.org/home/openknee.

• For each specimen, there should be a download package, which may have different release versions based on the availability of data and models, see ["Roadmap"], e.g.
  • Open Knee(s) Generation 2 - Specimen 1
• Different sections of specimen-specific data sets should be downloaded from the in-house data management site as compressed packages, e.g.
  • oks001-mri.zip
  • oks001-joint.zip
  • oks001-tissue.zip

• The compressed files should be uploaded to the appropriate download package at the "Downloads" section of https://simtk.org/home/openknee.

• The release version should be incremented based on the ["Roadmap"].