NeMO Week4

General information about the database

• What is the name of the database?

NeMO, The Neuroscience Multi-omic Archive

• What type of database is NeMO?
  • What biological information does NeMO contain?

NeMO focuses on single-cell genomic and transcriptomic data of various cells in the brain. (Via NeMO)

• • What type of data source does it have?

NeMO has primary data that is mostly electronically curated, but if something goes wrong before, during, or after an attempt to upload data, in-house NeMO team members are available to step in and help. (Via NeMO)

• What individual or organization maintains NeMO?

NeMO is maintained by the Institute for Genome Sciences at the University of Maryland School of Medicine, a large public institution.

• What are NeMO's funding source(s)?

NeMO is funded by NIDA, National Institute on Drug Abuse; and NIH, National Institutes of Health (Via NeMO)

Scientific quality of the database

• Does NeMO's content appear to completely cover its content domain?

NeMO currently holds 2,964,588 files from 562,696 samples. NeMO's owners recognize that this does not yet meet their goal of mapping every brain cell type in mammalian brains, and state that their database is ever-growing. Via NeMO Data Portal and Oxford University Press

• What species are covered in the database?

NeMO holds data from humans (adult and prenatal), mice, and non-human primates. While NeMO's main focus is mammalian brains, common model organism zebrafish has made its way into their public data pool. (Via NeMO Data Portal)

• What biological questions can NeMO help answer?

NeMO has sought to map all mammalian brain cell types. While this has not yet been accomplished, NeMO is on its way to its goals with over 50 million brain cell transcriptomes and epigenomes in their repository. (Via Oxford University Press)

• Is the database content timely?

Studying mammalian brains is helping scientists answer questions about the human brain. The NeMO database contributes to this research and makes information accessible to researchers and the public in this time of need. The NeMO archive is the only repository that hosts BICCN (BRAIN Initiative Cell Census Network) projects. (Via Oxford University Press)

• How current is the database?

NeMO went live in August 2018 and is updated soon after a user uploads data from a project relevant to NeMO's purpose. NeMO's data has likely been added to more recently, but their portal does not display latest updates nor upload dates on data for downloading. The NeMO homepage was updated on January 24, 2024. (Via Oxford University Press, NeMO Data Portal, and NeMO)

General utility of the database to the scientific community

• 1. Are there links to other databases? Which ones?
  2. Is it convenient to browse the data?
  3. Is it convenient to download the data?
     • In what file formats are the data provided?
       • What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
       • Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
  4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
     • Is the website well-organized?
     • Does it have a help section or tutorial?
     • Are the search options sensible?
     • Run a sample query. Do the results make sense?
  5. Access: Is there a license agreement or any restrictions on access to the database?
• Summary judgment
  1. Would you direct a colleague unfamiliar with the field to use it?
  2. Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, or seems amateur.