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NAHPU Documentation

First Day Using NAHPU

NAHPU simplifies recording and managing complex biological data, the environment that influences it, and the people who collect it. It is optimized for mobile and desktop screens and is designed to record natural history specimens both in the lab and in the field. In other words, NAHPU is more than a digital version of a paper catalog.

Key Concepts

Section titled “Key Concepts”

Understanding Projects

Section titled “Understanding Projects”

NAHPU organizes data by project. A project is a dataset, and what you consider as a project is up to you. It can be a field expedition, a collection of specimens prepared in a lab for a given year, or a long-term monitoring effort. If a single expedition covers several localities and each locality has its own reporting requirement, it often makes more sense to create one project per locality.

Each project has its own unique identifier (UUID) and is managed independently. Search, export, import, and data statistics all work at the project level. If your institution uses accession numbers, you can assign one to a project or reuse the same accession number across several projects, so they can be grouped into a single entity.

Site and Collecting Event Relationships

Section titled “Site and Collecting Event Relationships”

If you are coming from a paper-based catalog, this may be a new concept: think of a collecting event as the "session" during which specimens were collected, separate from the site where it happened.

A site holds information that usually does not change over a short period (typically up to a day), such as geography, habitat conditions, and coordinates. A collecting event holds the details that vary at a specific site during a specific period, such as the personnel involved checking traps, trap counts, weather, and astronomy data. It captures the effort, the people, and the environmental conditions at that time. Specimen records link to a collecting event rather than directly to a site.

Location, Locality, and Site Scopes

Section titled “Location, Locality, and Site Scopes”

These three terms are often used interchangeably within the museum community, and the ontologies behind them can lead to an "exhausting" debate. NAHPU keeps them at three scopes.

Location is the broad place that covers the whole project, and you record it in the project information. Locality is the precise place description stored in the site geography, and it is shared between sites so you can reuse it. Site is the narrowest scope. The camp, the hotel where you stay during an expedition, a net or trap line, and so on are all sites.

You can add any number of coordinates to a single site. When collecting with traps, for example, you can record a coordinate for each trap and assign a specimen to that coordinate. This gives specimen location down to GPS accuracy, which with a modern GPS can be as good as a 3 to 5 meter radius. The app also provides a coordinate extent field to estimate the distance from the recorded coordinate.

Controlled Vocabularies

Section titled “Controlled Vocabularies”

Controlled vocabularies are predefined lists of terms that keep data entry consistent, which is common practice in data management systems used by natural history museums. We did our best to align the default terms in NAHPU with terms used by collection management software such as Arctos, while still letting you customize them.

In the app they appear as dropdowns. Wherever a field draws on a vocabulary, such as site type, habitat type, coordinate datum, primary activity, collection method, personnel role, life stage, specimen condition, part type and treatment, and nearly every parasite field, you choose from a list instead of typing free text. The same term is then spelled the same way in every record.

The lists are yours to change and yours to share. Add terms, remove the ones you will not use, set a case format, then run Export user configs once so the whole team imports the same vocabularies. See Settings.

What if that sharing never happened? NAHPU still copes. Every dropdown also offers the distinct values already stored in the database, so nothing a colleague typed will break the app. A dataset can rebuild the vocabulary that produced it, which is exactly what reproducible records need.

Field Identifiers

Section titled “Field Identifiers”

The practice of assigning a unique identifier to a specimen in the field falls into three types: personal, institutional, and project-specific field IDs.

NAHPU supports personal field IDs through the cataloger role. Add your initials and current field number in the personnel form, and the app generates a unique field ID by combining them. The number is auto-incremented and can be overridden manually.

For the other two types, NAHPU's term for it is project ID. You can set a prefix, suffix, and starting number, with an auto-increment option.

Cataloger vs Collector Roles

Section titled “Cataloger vs Collector Roles”

NAHPU defines a collector as someone who collects a specimen but does not necessarily catalog it. This is a specific field in the specimen form, and anyone can be assigned to it with or without a specimen-care role. Your field guide who brought the specimen to you, or someone who donated an unprepared specimen to the collection, can be assigned as a collector.

A person who catalogs the specimen is a cataloger. This role provides access to field IDs, and a person with this role can also be assigned as a preparator, collector, or any other personnel field.

Shareability and Customization

Section titled “Shareability and Customization”

Almost everything in NAHPU is built to share and reproduce. Project records, the project identity and its UUID, taxon lists, personnel, controlled vocabularies, export presets, document templates, print layouts, and custom fields can all be exported and handed to somebody else. One person set NAHPU up the way your team works, export it once, and every device starts from the same conventions. That is NAHPU strength in reproducibility.

Most of it is only one QR code away. Larger things such as full projects, media, and the database are shareable as files, and NAHPU tells you when a record is too big for a QR code and offers the file instead. See Transfer a Project.

You can also export the project data in a simple tabular format, bundle in standardized formats, and export the records in PDF using your own layout design. All the exports and layout design can be done within NAHPU without any additional software. See Export.

Getting Started

Section titled “Getting Started”

  1. Set up NAHPU

    When you first install NAHPU, the setup button is visible on the home screen. If you do not see it or need to set it up later, you can access it through the menu drawer. The setup wizard walks through the catalog format, the field and tissue identifiers, the controlled vocabularies for sites, collecting events, and specimens, and whether you collect parasites. You can also import and export those settings, so setup only needs to be completed once for your entire team.

  2. Create a new project

    Use the + button in the bottom-right corner of the home screen and select New project. The setup wizard collects project information, offers an optional main taxon and field-ID setup, requests a Cataloger when personnel IDs are selected, and finishes with a review. The project name must be 3 to 25 characters long.

    You can skip device setup and complete it later in Settings. See Projects for the complete wizard and project-information import workflow.

    After the review, Create project opens the dashboard.

    NAHPU generates a project UUID for every new project. We use UUID version 4. When you import project information from another device, NAHPU retains the imported UUID.

  3. Get to know the dashboard

    The dashboard is the main project interface. It is divided into four panels.

    • The top-left panel is the project overview. Use Edit and Export info to manage project information. Use Export project when you need to transfer records and media.
    • The top-right panel contains personnel data. Use this panel to add and manage personnel for the project. Personnel appear as a list in this panel after they are created.
    • The bottom-left panel is the taxon registry. Use this panel to add and manage taxon information for the project.
    • The bottom-right panel contains the record statistics. It shows the number of records added to the project. Select Explore more stats for detailed charts, tables, and filters.

  4. Add new personnel

    Every project needs at least one Cataloger. The create-project wizard asks for one as soon as you choose personnel field IDs, and it will not let you finish without one. The cataloger owns the field number that generates each specimen's field ID, so add this person before you start cataloging. Once that is done, add as many other people as the project needs.

    • Cataloger is responsible for cataloging the specimen. Their initials and field number generate the Field ID on the specimen catalog page. Their name also appears wherever a field asks for personnel, such as collecting personnel and preparator. The app does not allow you to change the cataloger role after it is created.

    • Determiner only is a person who identifies specimens but does not catalog or prepare them. Select them in the specimen form's Determiner field.

    • Preparator only is a person who helps prepare the specimen but is not involved in managing the data. Their name does not appear in the cataloger field on the specimen page, but it can appear elsewhere, such as in the Preparator and Collecting personnel fields.

    • None is reserved for personnel who are not directly involved in specimen care. NAHPU aims to ensure that everyone involved in the field is recorded in the field data. You can assign this role to your driver, local guides, cooks, and others. Their names appear only in the Collecting personnel field. If they are involved in obtaining a specimen, you can also associate them as a collector.

  5. Add a new taxon

    You can add a taxon manually using the Add taxon button or import it from a file. The preferred formats are .xlsx, .csv, and .tsv. NAHPU will make a best-effort attempt to parse other file types.

    Manual entry and file import both support class, order, family, genus, species, and subspecies records. In an import file, add a taxon rank column. You may omit it only when class, order, family, genus, and specific epithet are all present, in which case the row defaults to species.

    • For recognized delimited files, the app selects the delimiter by extension (.csv = comma, .tsv = tab).
    • For unrecognized extensions, auto-detect tries Excel, comma, tab, and semicolon first. If that fails, use the advanced parser override and enter a custom raw delimiter.
    • .xlsx has the best support; older or other Excel formats may fail.

    Each row requires the classification columns from class through its selected rank. A subspecies row therefore also needs subspecific epithet. You can include authors, common name, IUCN Category, CITES status, country status, sorting order, and notes. The app automatically detects supported header aliases, such as taxonRank, taxonClass, taxonOrder, taxonFamily, specificEpithet, and infraspecificEpithet. You can manually select the column type using the dropdown menu if the app does not automatically assign the correct type to each column. Other columns are ignored.

    Example taxon import table:

    | taxon rank | class    | order    | family  | genus   | epithet   | common name       |
    | ---------- | -------- | -------- | ------- | ------- | --------- | ----------------- |
    | species    | Mammalia | Rodentia | Muridae | Bunomys | coelestis | Heavenly hill rat |
    | species    | Mammalia | Rodentia | Muridae | Bunomys | penitus   | Inland hill rat   |

  6. Create a site

    Navigate to the site page using the navigation bar. To create a new site, use the + button in the top-right corner. Fill in at least the Site ID. The app limits the Site ID to 20 characters and enforces uppercase formatting. You will refer to this ID throughout the record form whenever it asks for a site.

  7. Add a narrative

    This is your field journal. It is good practice to write a narrative every day, and you can write about anything that happened that day. Navigate to the Narrative page using the bottom navigation bar and select +. Add the date, time, site, writer, and Markdown-supported narrative text. Plain text is fine; when a long entry reads better with headings, lists, or emphasis, the Markdown cheat sheet shows everything the narrative editor understands. You can also attach media and search or preview entries later. See Narrative.

  8. Add collecting events

    To create a collecting event, use the + button in the top-right corner of the collecting event page. Select site ID, start date, start time, end date, and end time. Then fill out the rest of the form.

    The app combines the Site ID and start date to create a unique ID for each collecting event, such as GP-L1-March, 23 2023. You will use this ID to refer to the collecting event in the specimen record. If you run multiple collecting events at the same site on the same day, add a suffix to distinguish them, such as Line1-Mar 26, 2023-1, Line1-Mar 26, 2023-2, Line1-Mar 26, 2023-day, or Line1-Mar 26, 2023-night.

  9. Add specimen records

    To create a specimen record, use the + button in the top-right corner of the specimen-record page. NAHPU generates the record in the currently active catalog format. The only difference between catalog formats is the measurement fields. After creating a new specimen record, fill in the relevant information, then repeat for the next specimen.

  10. Export records

    To export records, go to the dashboard menu, indicated by the hamburger icon (three horizontal lines) in the top-left corner. You have multiple export options:

    • Export records. Choose a tabular export preset and write one record type to .csv, .tsv, .xlsx, or .json. This is highly customizable, and you can create your own export presets. The preset sets the record type, the headers, and the field mapping. See Export records.

    • Bundle records. Create a Darwin Core Archive, Darwin Core Data Package, or complete NAHPU Data Package. Data Packages can use TAR.GZ or ZIP. This is useful for sharing data or analyses in a standardized format. See Bundle records.

    • Export documents. Produce labels, tags, catalog prints, and other printable documents as PDF from a document template and a print layout. You can designed your own layout in a WYSIWYG editor bundled in the app. See Export documents.

  11. Back up your project

    Like any digital data, regular backup is recommended. NAHPU offers two backup options: project export and database backup. For fieldwork, at the end of each field day, we recommend exporting the project. Open the dashboard menu and select Export project. Choose ZIP or TAR.GZ so the available media bundled with the records, or turn on Light export for a small JSON.GZ when the upload has to fit a weak connection. Having a project export copy somewhere other than the working device and a cross sharing with team members are recommended for redundancy.

    Alternatively, select Backup database instead. Choose TAR.GZ or ZIP. The archive holds the database and every file in NAHPU app data, whether or not a project links to it. In the field, run it occasionally, when battery use is not a concern.