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Using Metadata in LabTrove

Using metadata effectively in LabTrove can help you to organise your research. It can be used to group related notebook entries and to enable you and others to more easily find your work.

Introduction to metadata​

What is metadata?​

Metadata is data that describes the attributes of other data. For example, a photograph might have the following metadata:

  • Time and date the photo was taken
  • The size of the image
  • The resolution of the image
  • The camera that took the photo
  • The aperture and shutter speed settings
  • The lighting and flash settings
  • Who took the photo
  • Who is in the photo
  • What is the subject of the photo
  • What colours are in the photo
  • Where the photo was taken

Metadata can be automatically generated by some technology, or it can be defined by the creator or user of that data. In a photograph the resolution, size, date and time, camera settings, and camera that took the photo, are all automatically captured and added at the point the photograph is taken. Other metadata, for example, who took the picture and what the subject of the photograph is may have been added by a user, for example in the form of tags or keywords added to the photograph.

Using metadata is a way to categorise or classify your data, making it easier to find and manipulate. For example, if you have added metadata to your photographs to the subject of the photo, it is easy to find all the photos including that subject and exclude all photos that do not contain that subject.

For more information about metadata, see Metadata.

Metadata in the laboratory​

Descriptive and preservation metadata are particularly important for data-driven science. Understanding and working with large data volumes is difficult without appropriate metadata or, to be precise, descriptive metadata. It is particularly important to capture - with metadata - the process by which scientific data is obtained: results should always be open to testing and be capable of replication. The relationships between objects – the research elements – are an important feature of the research process, as are the histories of each object. The digital provenance of research data consists of these relationships and histories.

The scholarly communication process relies not only on publishing analyses and conclusions, but also on the availability of the research outputs. To ensure the value and reusability, researchers must curate those outputs by capturing appropriate metadata. Designing curation into experiments is an effective solution to the provision of high-quality metadata that leads to better, more reusable data and to better science. For more information, see Curation of Laboratory Experimental Data as Part of the Overall Data Lifecycle.

Why should I use metadata?​

Using metadata when recording your experiment enables others to find that information, view the information that is linked together, which helps them to reuse the information and to replicate your experiments. Using metadata effectively also supports your own work, by enabling you to find your data easily in the future, to organise your data, and to help link related data together. Using metadata when you create your content enables you to locate that information without needing to trawl through everything in order to find it. You can filter out the content you don't need right now in order to narrow down the results to search through.

Using common metadata across a team helps the team to link their data together, and ensures consistency between experiments and projects.

Metadata in LabTrove​

When you create a record of your experiments using LabTrove, some metadata is automatically created for you, but you can also add your own metadata to help you classify your data for future use. For Entries you create, the following metadata is automatically captured:

  • Date and time of creation
  • Date and time of updates
  • A unique ID for each version
  • Author

Sections​

There is one piece of metadata that you must define as a user. For each Entry you create, you must assign the Entry to a Section. You can create and define your own Sections. The Section is useful for indicating what type of Entry you are writing, for example:

  • Risk assessment
  • Safety
  • Instrument instructions
  • Reaction scheme
  • Procedure
  • Products
  • Reagents
  • Analysis
  • Yield
  • Results
  • Discussion

The different Sections that you create are displayed as links beneath the Section heading in the right hand navigation menu of each Notebook. Next to each Section title is the number of Entries that have been assigned to that Section. If you click on the name of the Section, a list of all the Entries that are classified as being that kind of Entry are displayed.

The Sections that you create will depend on the kinds of experiments and writing that you intend to do. It is helpful if a team are undertaking similar research that they have consistent metadata, including Sections.

Templates​

There is a specific kind of Entry called a template that can be used to standardise the content of Entries. A template is created from a Entry by assigning it to the Section called Templates. A Entry that has Templates as the Section name is treated in a different way to a normal Entry and can be used to create a new Entry. For more information about templates, see Recording_repeated_processes.

Metadata keys and values​

In addition to adding a Section to your Entry, you can add more metadata in the form of key-value pairs. The key represents the attribute of the data, and the value is the value assigned to that attribute. For example you could create a key of Instrument and use different values depending on the instrument used in the experiment. Other examples of keys you might use are:

  • Analysis type
  • Experiment type
  • Project name
  • Method
  • Reagent
  • Product
  • Molecule
  • Compound
  • Sample
  • Experiment code
  • Procedural step
  • Source
  • Enzyme
  • Background

You can add as many key-value pairs as you need to your Entry to describe its content. It is helpful if a team are undertaking similar research to have consistent metadata, including using the same keys.

The different keys that you create are displayed as main headings in the right hand navigation menu of each Notebook. The values are displayed as a list of links under each of these main headings. Next to each value link is the number of Entries that have been assigned that value for the key. If you click on the value, a list of all the Entries that are classified as sharing that value are displayed.

Defining the metadata for your experiment​

Choosing metadata​

You need to be consistent about the metadata that you use for your research project or Notebook. The metadata will need to be tailored to your project, but teams and individuals that are undertaking the same research goals or experiment types should benefit from a consistent metadata design. Coming up with a good design in advance for your metadata might be difficult, but it is easier than changing all the metadata later on, or adding metadata to a Notebook that doesn't use it.

You can try out your metadata design by creating a new Entry containing the different keys and values. You could also create a Entry for each different Entry type you expect to use, and add key-value pair metadata that is relevant to that type of Entry.

Editing metadata​

You can change the names or values for metadata that are displayed in the right hand navigation menu by editing the content within the Entries. if all Entries that refer to a Section or key heading are changed to remove that name, the name is removed from the navigation menu. To change the name of a Section or key heading you must update every Entry to which the metadata is linked. It is easier to make these changes early in the life of the Notebook when there are not many posts to update.

Choosing Sections​

Each Entry must be added to one Section. The Section is useful for indicating what type of Entry you are writing. Create distinct categories for your Sections:

  • Select broad, easily-understood categories (preferably from a shared list)
  • Choose non-overlapping categories You might need to create extra Sections as time goes on and as more Entrys are added. For example, if the activities in the project change or new techniques are explored.

Choosing keys​

Each post can be assigned metadata key-pair values. These metadata items are useful for organizing your posts and making them easier to find. Unlike Sections, you can assign multiple key-value pairs as metadata for your Entries. The following list provides some suggestions for choosing keys and selecting associated values:

  • Select broad categories to use as keys
  • Define a number of values to divide each key into meaningful sub-categories
  • Create categories that represent different ways of searching. For example, instrument and material.
  • Plan your metadata so that each category contains a manageable number of blog posts:
    • Avoid creating keys that are too broad, if most of your Entries fit into one or two categories it will be difficult to search through them to find your data.
    • Avoid creating overly specific keys. If you have a very large number of keys with only one or two values the navigation menu can become very complex, and it will be more difficult to find your data.

Creating consistent metadata​

Metadata is very valuable for ensuring consistent data collection and recording for teams, and also helping to link together work being done one related topics. Defining and standardising your metadata and sharing across the team prevents the introduction of inconsistencies. It also makes it easier to use because individuals do not need to create their own metadata designs and the intri The following is a list of tips for creating consistent metadata in teams:

  • Create or use a Template Entry to define consistent metadata for the team or group.
  • Define a standard list of Sections appropriate for your project or area.
  • If these are not included in your Section list, create a metadata key for the experimental activity or stage, and define a standard list of values.
  • Create metadata keys and standard values for items like:
    • Instruments
    • Reagents
    • Materials
    • Methods
  • Create metadata keys and standard values for departmental metadata such as sample IDs, experiment codes, batch numbers, and references.

There are some standard vocabularies that can be used to help, for example:

  • Properties Ontology (ChemAxiomProp) – 150+ chemical and materials properties
  • Measurement Techniques (ChemAxiomMetrology) – 200+ measurement techniques

For more information, see: [ChemAxiom: An Ontology for Chemistry 2. The Set-Up] (http://semanticscience.wordpress.com/2009/04/08/chemaxiom-an-ontology-for-chemistry-2-the-set-up/).

Adding metadata to your notebook entries​

Every Entry that you create must be added to a Section. In addition to the Section, you can add more metadata to your Entry in the form of key-value pairs. The key represents the attribute of the data, and the value is the value assigned to that attribute.

For more information about the metadata you can add to your Entries in LabTrove, see Using metadata. For help defining the metadata for your Notebook, see Defining the metadata for your experiment.

Adding your Entry to a Section​

You can choose a Section from the existing options in the drop-down list, or alternatively you can create a new Section:

  1. Create or edit a Entry
  2. Select - New section - from the drop-down list.
  3. Enter a name for the new Section in the New section name.
  4. Click OK.

A new Section is created in the Sections part of the navigation menu in the Notebook. Your Entry is added to the new Section. The Section is available in the drop-down menu for Section when you create or edit a Entry.

Adding metadata to your Entry​

You can add metadata to your Entries in the form of key/value pairs. The key is displayed as a heading in the navigation menu and the value becomes a link beneath that heading. For example you might create a key called Data with a value of NMR. You can add multiple key and value pairs to your Entries. To add metadata key and value pairs to your Entry:

  1. Create or edit a Entry
  2. In the Extra Metadata section select an existing value for key or alternatively create a new key:
    1. Select -- New Key -- from the drop-down list.
    2. Enter a name for the new key in the New metadata key.
    3. Click OK
  3. Add a new value for the selected key in the value text box.
  4. (Optional) If you want to add multiple values to the same key, add the values separated with semicolons. For example:Sample;Product
  5. Click the Add metadata button. A new row with key and value options is displayed below the key and value you created.
  6. To add more metadata keys and values, repeat the process above, clicking the Add metadata button for each new entry.
  7. Click Submit to save the Entry with the metadata.

What to do next: