adding field notes documentation #125
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still need to add new screen shots |
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to be discussed: the functionality section of the submission portal provides a LOT of background and general information abotu things like GSC and standards while the field notes is just a step b step.. based on diataxis.. should these be split out? @cmungall maybe you could take a look and give me your thoughts on how much information / what information should be where as related to https://docs.microbiomedata.org/howto_guides/submit2nmdc.html#portal-functionality |
pkalita-lbl
requested review from
simroux,
pkalita-lbl and
eecavanna
and removed request for
eecavanna
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@mslarae13 : Looking good to me ! Just added a few suggestions and some typos/etc.
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| ## Introduction | |||
| The NMDC Submission Portal (https://data.microbiomedata.org/submission/home) was released in April 2022. It is designed to lower barriers to capture metadata and adhere to community standards, addressing the critical gap of collecting necessary metadata describing a study and its biosamples. The Submission Portal is designed using a flexible framework leveraging a new modeling approach called the Linked Data Modeling Language (LinkML) and the template-driven spreadsheet tool DataHarmonizer. It supports several different community standards, such as the Minimal Information about any (x) Sequence (MIxS) standard from the Genomic Standards Consortium (GSC), the PROV standard for provenance metadata, the Proteomics Standards Initiative (PSI) standards for metaproteomics, and the Metabolomics Standards Initiative (MSI) standards for metabolomics. The Submission Portal is an intuitive interface that allows researchers to provide information about their study, the metadata about the study’s biosamples, multi-omics data associated with the study, and whether Department of Energy (DOE) user facility proposals are associated with the data. Updates and new features are continually being implemented as user research provides new insights to improve usability, and as standards are updated and improved. | |||
| The NMDC has developed 2 products for improving metadata capture. The NMDC Submission Portal (https://data.microbiomedata.org/submission/home) (released April 2022) and NMDC Field notes (currently in beta testing) are designed to lower barriers to capture metadata and adhere to community standards, addressing the critical gap of collecting necessary metadata describing a study and its biosamples. | |||
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"2 products" -> "two products" ? (looks like we currently spell out these numbers)
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| This app is designed to streamline real-time registration and collection of standardized metadata and field measurements. | ||
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| Each section of the app will automatically launch a quick walk-through. You can press the → button to continue the tour or press the X button to end it. To re-initiate the walk through at any time, visit the Settings page and select ‘App Walk-Through’ |
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"Each section" -> "Upon first use, each section"
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| The Field Notes App requires ORCiD authentication to access. | ||
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| Submissions via Field Notes are available in the Submission Portal as an automatic backup when connected to wifi. The app is available for offline use, but requires internet connection to **start** a submission. |
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Maybe "Submissions via Field Notes are available in the Submission Portal as an automatic backup when connected to wifi" could be "Data entered via Field Notes are automatically synced and available in the Submission Portal when connected to wifi or cellular network".
To be check by @pkalita-lbl , but I believe this sync is active as soon as there is an internet connection, no matter if wifi or else ?
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| [](../_static/images/howto_guides/portal_guide/Create_submission.png) | ||
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| Once signed in with an ORCiD, you will have the ability to access existing studys or create a study using the 'New’ button. Details about each section are outlined below. Users can also return to existing submissions saved under the ORCiD account to resume their work at any point. |
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| The Study Information page requires a valid ‘Study Name’ and a valid email address. All other fields are optional and can be completed in the app or in the Submission Portal. Study names and all other information can be updated or added via the app or Submission Portal. See [header](#submission-portal-functionality) [header](#study) for more details about Study information. | ||
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| Also in the New Study you will select your "Environment Template". This will correspond to the GSC Environmental Extension. More information is available above in sections [header](#environmental-package). Multiple environments can be selects and submitted in one submission. |
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"the GSC Environmental Extension." -> "the GSC Environmental Extension that best fits your samples." ?
"can be selects" -> "can be selected"
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| In Field Notes, sample metadata are entered individually in a form like structure. This is different than the grid format of the Submission Portal | ||
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| The Sample (TODO Biosample in Submission Portal vs Sample here?) Metadata interface consists of a form like structure where metadata is entered individually, unlike the grid format of the Submission Portal. |
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I would maybe only keep this one ("The sample ... Portal") or the previous one ("In Filed Notes ... Portal"), but not both ?
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| The Sample (TODO Biosample in Submission Portal vs Sample here?) Metadata interface consists of a form like structure where metadata is entered individually, unlike the grid format of the Submission Portal. | ||
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| Required metadata is marked with a ⚠️ symbol. Though, no metadata can be provided and the same will still be saved. |
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maybe "no metadata can be provided" -> "these fields can be left empty" ?
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| ##### Location Provided Metadata | ||
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| Field Notes can use your mobile device information and location to populate some metadata fields. For example, selecting "Set to today" for the term "collection date" will auto populate with the current date. Additional, mobile GPS coordinates can be used to populate "latitude and longitude" field by selecting "Use GPS location". This along with other auto-populating fields ensure accurate and structured metadata in real time and minimuzes human error. |
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"Additional" -> "Additionally" ?
"minimuzes" -> "minimizes"
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Hi @mslarae13, I'll hold off on reviewing this until you've addressed the feedback @simroux left above (whichever pieces of that feedback that you are planning to address). That way, I'll still have a "fresh pair of eyes" (not reading so much on autopilot due to having seen it before) at the time. |
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