Data for Data Science Week 3: Documenting data with metadata
Today’s objectives After today’s class, you should be able to: Understand the utility of metadata, both during active research and after project completion Identify different types of metadata and their utility Outline metadata for your own research project
Activity: What would you need to know to use these data? Have you ever tried to use someone else’s data?
What kind of metadata do we need for each level of data complexity?
Metadata: data about data Metadata: the information we create, store, and share to describe things NISO (National Information Standards Organization) defines three types of metadata Descriptive: finding and understanding a resource Administrative: technical, preservation, and rights (licensing) information Structural: relationships of parts of resources to one another Understanding Metadata
Metadata for scientific research projects Intent: what is the project? Collection method: how was the experiment conducted? File structure: where are files located? Data type: what is the file type and format? Data description: what do columns/rows mean? Provenance: how have data been manipulated?
What do the metadata for these data include? Rodent metadata Metadata for the entire project (rodent, plant, ant, precipitation)
Activity: What are the metadata, and where are they found? GEO example
How do we document metadata? Include READMEs! One README per data file/set, as .txt file, named to reflect data file Format README files consistently Use standardized dates, and vocabulary that is convention for your field
Guide to Writing READMEs
README: General information Provide a title for the dataset Name/institution/address/email information for Principal investigator (or person responsible for collecting the data) Associate or co-investigators Contact person for questions Date of data collection (can be a single date, or a range) Information about geographic location of data collection Keywords used to describe the data topic Language information Information about funding sources that supported the collection of the data Guide to Writing READMEs Items in bold are most important
README: Data and file overview For each filename, a short description of what data it contains Format of the file if not obvious from the file name If the data set includes multiple files that relate to one another, the relationship between the files or a description of the file structure that holds them (possible terminology might include “dataset” or “study” or “data package”) Date that the file was created Date(s) that the file(s) was updated (versioned) and the nature of the update(s), if applicable Information about related data collected but that is not in the described dataset Guide to Writing READMEs Items in bold are most important
README: Sharing and access information Licenses or restrictions placed on the data Links to publications that cite or use the data Links to other publicly accessible locations of the data (see best practices for sharing data for more information about identifying repositories) Recommended citation for the data (see best practices for data citation) Guide to Writing READMEs We’ll talk more about licenses next week! Items in bold are most important
README: Methodology Description of methods for data collection or generation (include links or references to publications or other documentation containing experimental design or protocols used) Description of methods used for data processing (describe how the data were generated from the raw or collected data) Any software or instrument-specific information needed to understand or interpret the data, including software and hardware version numbers Standards and calibration information, if appropriate Describe any quality-assurance procedures performed on the data People involved with sample collection, processing, analysis and/or submission Guide to Writing READMEs Items in bold are most important
README: Data-specific information Count of number of variables, and number of cases or rows Data dictionary: Variable list, including full names and definitions (spell out abbreviated words) of column headings for tabular data Units of measurement Definitions for codes or symbols used to record missing data Specialized formats or other abbreviations used Guide to Writing READMEs Include a README like this for each file/dataset Items in bold are most important
README: Data-specific information We often use data published by other researchers (such as the human genome sequence). Metadata for your analysis in these cases should include: Where the data can be found, including a URL and data citation (if applicable; this information may be referenced in the license) How the data (from the original URL/source) were filtered/transformed/manipulated as a part of your analysis
Guide to Writing READMEs
How do we document biomedical metadata? Types of metadata: Reagent: clinical samples, biological reagents, chemical reagents Technical: auto-generated information from research instruments/software Experimental: protocols, conditions, equipment Analytical: data analysis methods, including software name/version, quality control parameters, output file types Dataset: project objectives, personnel, publications, funding Harvard Biomedical Data Management
How do we document biomedical metadata? Include information about IRB approval Data security: consider where data are stored and who has access Document data that exists, but may not be stored with a given project File naming conventions can assist in documentation Recommended directory structures for large-scale projects can reflect components of metadata Harvard Biomedical Data Management
Metadata and the data life cycle
Documenting information about a dataset and/or project is a part of the life cycle Metadata facilitates all parts of the life cycle Primer on Data Management
GDC Data Portal Activity: What data are available from the GDC Data Portal? Where can you find the metadata? Who can use these data?
Why does metadata matter?
What questions do you have about documentation of metadata for your projects?
Summary Metadata includes multiple types of information, some of which may not seem important while conducting the research, but are essential for others being able to understand it Every data file should have an associated metadata file that describes it Some metadata is better than no metadata! Most metadata represents things you’ll need to include in a publication (or other deliverable), so document early and often
Next time: data manipulation and reproducibility
Resources Guide to writing “readme” style metadata from Cornell University Harvard Biomedical Data Management: Metadata overview, READMEs
Allow 5-7 minutes to work on each activity, then regroup and discuss as class
Activity (spreadsheet): What would you need to know to use these data?
Activity (GEO): What are the metadata, and where are they found?
Activity (GDC): What data are available from the GDC Data Portal?