Brief description of all of the defined tags in MEDFORD. Click each tag to view the in-depth description of the tag purpose and what sub-tags are available.
Every tag in MEDFORD has the <tag>-Note sub tag unless specified otherwise, which can be used for other information about the tag that the author may find relevant, but not within the scope of the other sub-tags.
- Contributor: Tag to describe any individual that is involved in the project.
- Data: Tag to describe data sets in the project, such as RNA-Seq data. Can be either referenced (a link to a data set generated by someone else) or recorded (new data from this project.)
- Date: A tag to store some sort of date, such as paper submission or acceptance.
- Expedition: A tag to describe the trip in which data was collected, such as a cruise for coral data.
- Funding: A tag to describe funding sources involved in the research.
- Journal: Describes the journal in which this project is published, if applicable.
- Keyword: Contains a keyword that can be used to search for this MEDFORD file that is considered relevant to the research within.
- Method: Describes methods used in this research, such as DNA extraction kits.
- Paper: Accession information for the published location of this research, if applicable.
- Project: Brief description of the research stored within this MEDFORD file.
- Software: Software used in the research described by this MEDFORD file, such as rna-seq software.
- Species: Species involved in the research, including locality information if applicable.
- Structure: Details about the overall structure of this particular MEDFORD file.
All tags described in this document have some form of validation. If an author wants to add data that may not validate but fits under one of the describe tags, it is recommended to use the 'Freeform' prefix. This signals to the MEDFORD parser that this tag is not to be validated nor indexed.
A date could first be written in freeform format while at the field:
@Freeform-Date Jun 19 - Took sample
Later, in the lab, this can be adjusted to follow standard Date formatting and replaced with:
@Date 2021-06-19
@Date-Note Obtained sample #42 from reef #3
Example of what BCO-DMO needs here.
A contributor tag is used to describe either an individual involved in the research described by this MEDFORD file. A contributor is not necessarily an author but may be some other collaborator, such as an individual who performed the sample collection.
- Contributor: (REQUIRED) The name of the contributor.
- Contributor-ORCID: The ORCID of the contributor, if applicable.
- Contributor-Association: The name of the association of the contributor.
- Contributor-Role: A string explanation of the role of the contributor. This can be a standardized value, such as "First Author", or a string description of choice, such as "Sample collection at Hawaii Reef"
- Contributor-Email: An email the contributor can be reached at.
A tag describing a data set involved in the research within the MEDFORD file. All data, be it new or a reference to existing data, should have its own data tag, as the purpose is for future readers to be able to know exactly which dataset and what version of the dataset was used.
The sub-tags are as follows:
- Data: (REQUIRED) A description of the data.
- Data-Type: (REQUIRED) A string describing the way the data is stored in relation to this MEDFORD file. 'Website', 'Database', 'Github' are some examples.
- Data-URI: If applicable, the URL to the data. This could be a github repository link or a database link.
- Data-Flag: 'recorded' or 'referenced'; a description of whether the data is new to the research within this MEDFORD file ('recorded') or taken from another source ('referenced'). This is set to 'referenced' by default.
An example of how RNA-seq data generated for the research within a MEDFORD document would be:
@Data P.damicornis RNA-seq
@Data-Type ???
@Data-Flag recorded
An example of data stored within a database would be:
@Data NCBI Pocillopora damicornis genome
@Data-Type Database
@Data-URI https://www.ncbi.nlm.nih.gov/genome/?term=Pocillopora+damicornis
A tag describing dates of interest for the research within the MEDFORD file. Common examples include: date submitted for publishing, date accepted for publishing, and date published. Dates should be written in the following format:
- Date: (REQUIRED) YYYY-MM-DD format date.
- Date-Note: A description of the relevance of the date.
The date this example was written would be documented as follows:
@Date 2021-03-02
@Date-Note Published
A funding tab is used to describe a grant or other funding source used in the research described by the MEDFORD file.
- Funding: (REQUIRED) The name of the funding source.
- Funding-ID: The ID of the grant.
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Structure tags define file-wide settings about the specific MEDFORD file being written. For example, setting the TimeZone structure tag will define what time zone all times are written in.
The sub-tags are as follows:
- TimeZone: The time zone all dates are written in in this file. They should be written in the standard time zone abbreviation, such as GMT or EST. The defined time zone is GMT.