NeMO Week4

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Week 4 NeMO presentation

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. (Via NeMO)

  • 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?
      • Yes, the resources page contains links to BCDC (brain cell data center), it also has contains links to GitHub which contains additional documentation for NEMO, as well as a link to Terra, an online platform for biomedical research resources
    2. Is NeMO convenient to browse the data?
      • Yes, and no. The portal has three different tabs to browse the data. Those being Home, Studies, and Data. Although, using the data portal is quite difficult. Every time a filter is added or something is added to the search the site takes a long time to load, likely because the site does a query on the database every time something is added as opposed to having searches pre-saved. via NeMO
    3. Is it convenient to download the data?
      • Downloading the data has the same problems as navigating the data. It takes a long time to filter through data results to find the file that you want downloaded. Once the file is selected it is relatively easy to download the file. All you need to do is add it to your cart and then download it. Although the files are usually very large. data portal
      • In what file formats are the data provided?
        • What type of files, indicated by the file extension?
          • The three most common file formats are TSV, FASTQ, and BAM. data portal
        • Are they standard or non-standard formats?
          • Yes they are, FASTQ is the standard format for sequences, TSV is also a standard form for text based data, BAM is another standard form for representing data sequences, it is in binary, however data portal
    4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
        • Yes, a naive user likely navigate the site as easily as an experienced user. Meaning that the search options are easily identifiable, but the problems with the site would be as much of a problem for an experienced user, for it will take just as long to load the results for anybody using the site. More experience cannot fix the fact that the database has a design flaw in the way that it runs queries every time anything is added to the filters. data portal
      • Is the NeMO website well-organized?
        • Yes, the search options are easily identifiable and it is easy to find how to get to the data portal or to other places in the database home page.
      • Does it have a help section or tutorial?
        • Under the data tab of the website, there are other pages that tell the steps of downloading public data data downloading, and accessing controlled data accessing controlled data although there are no videos or direct tutorials for using the data portal, which may have been helpful, because there are some sections and probably lots of jargon that are unfamiliar to a naive user.
      • Are the search options sensible?
        • In some ways yes, because they do make sense at first glance, such as the different filter options. Such as the different brain regions and sub regions, but they often contain jargon that even I am unfamiliar with. They also contain many options, in some cases, up to 800 data portal.
      • Run a sample query. Do the results make sense?
        • Yes, I ran a search with the filters on the human organism and in the amygdaloid complex, it still gave me about 50,000 files to choose from. It also takes a long time for the website to load and for each filter and search to refresh. Likely because they actually run a query every time you do a search search result.
    5. Access: Is there a license agreement or any restrictions on access to the database?
        • The database has three main categories of data, public, embargo, and restricted. Embargo data has to be held back until a specific time at which it can be released to the public. Restricted data can only be distributed to a select few individuals upon approval different types of data
  • Summary judgment
    1. Would you direct a colleague unfamiliar with the field to use NeMO?
      • I would probably not direct a colleague unfamiliar with this material to use this database, for I have a hard time searching for things on the database as a relatively experienced user. There is much jargon on the database that I am unfamiliar with and therefore do not understand about it. For this reason, I believe that someone unfamiliar with the field would have an even harder time navigating it. NeMO is of little use to someone not focused on brain mapping or brain cell transcriptomics or epigenomics.
    2. Is this a professional or "hobby" database?
      • The NeMO archive database is a professional database. It is associated with and supported by the NIH, a US government organization.

Acknowledgments

Dean Symonds and Hailey Ivanson worked together on NeMO Week 4. Dean found the database from the list provided by Dr. Kam Dahlquist. The homework partners split the Week 4 questions and presentation up evenly, with text communications on 2/3/2024, in-class work on 2/5/2024, and video chat and text communications on 2/7/2024 to collaborate on the work assigned. Discussion in class on 2/5/2024 with Dr. Kam Dahlquist led to information included on why we believe the NeMO archive takes so long to load.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

Hivanson (talk) 22:42, 7 February 2024 (PST)

Template:Hivanson

Dean

I utilized my homework partner, Hailey Ivanson for this assignment. We texted over the weekend to determine who would do which questions and when we would start our slides. We also worked on our slides in class on Tuesday and utilized our professor, Dr. Dahlquist during class. Hailey and I also FaceTimed on Wednesday night to discuss our slides. Except for what is noted above, this individual journal entry was completed by me and not copied from another source Msymond1 (talk) 22:41, 7 February 2024 (PST)

References

  • Ament, S. A., Adkins, R. S., Carter, R., Chrysostomou, E., Colantuoni, C., Crabtree, J., Creasy, H. H., Degatano, K., Felix, V., Gandt, P., Garden, G. A., Giglio, M., Herb, B. R., Khajouei, F., Kiernan, E., McCracken, C., McDaniel, K., Nadendla, S., Nickel, L., … White, O. R. (2023). The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain. Nucleic Acids Research, 51(D1), D1075–D1085. https://doi.org/10.1093/nar/gkac962
  • LMU BioDB 2024. (2024). Week 4. Retrieved February 7, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_4
  • Neuroscience Multi-Omic (NeMO) Data Portal. (2024). Retrieved February 7, 2024, from https://portal.nemoarchive.org/
  • NeMO Archive—Home. (2024). Retrieved February 7, 2024, from https://nemoarchive.org/

User Page

Assignment Pages

Individual Journal Pages

Class Journal Pages

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