Minutes_MiniStd_2020 02 - airr-community/airr-standards GitHub Wiki

MiniStd Call 2020-02

Agenda

Follow-up

  • Object definition for receptor and cell (in #320, also see Christian's comment of 2019-12-24 in #273)
  • List of To-Does for MiAIRR v2 in #305
  • Should fields be non-nullable based on the availability of the information to the primary data depository (current situation) or the necessity of the information for meaningful interpretation? Note that the current situation can make it hard for third-party annotators #310.
    • A few things non-null "could" indicate:
      • Criticality to MiAIRR as a Standard - things one MUST always have as decided by the AIRR Community.
      • Things one should always be expected to have - not necessarily critical to MiAIRR but hard to understand how one could do a study and not have it.
    • Note that many of the non-nullable fields are controlled vocabularies with NULL-like options such as library_generation_method:other and physical_linkage:none. Perhaps for non-nullable fields this should be the norm. We should consider carefully those fields that have limited possible values (booleans, controlled vocabularies with no null-like possibilities) and ensure that if they do not exist we really want that to data be not AIRR- compliant.
  • DataRep decision on organism field
  • Should we switch notes from Google Docs to Github?
  • Review CEDAR Templates
    1. Confirm it is OK for the template, and the elements it is based on, to be publicly visible
    2. Confirm plan to have CEDAR's Version attribute not track MiAIRR version (which will be captured in title and description)

New Topics

  • Use of x-airr attributes in specification #297
    • X-airr: required
    • How important is this to MiAIRR?
      • Current understanding is that all MiAIRR fields are "required" but many can be NULL. So when describing a study, the fields should always be present. There is discussion around the spec about making it possible to have a null object in the specification (e.g. Diagnosis), which means that an AIRR Repertoire JSON file may not have all of the MiAIRR required fields (see #328) (e.g. disease_diagnosis may not exist in the JSON description). From a specification of a study, this seems to make sense (if you do not have any diagnosis you do not have any of these fields) but from a MiAIRR perspective, the understanding is that it is desirable to have these fields present (for easier validation).
  • Split of read_length field (#324 as fix for #279 )
    • Field read_length still exists, but its type has changed and it now is an integer and only represents read length in one direction.
    • There is now a new paired_read_length field that is an integer that represents the read length in the paired direction.
    • Field read_length was originally in the Schema object SequencingRun and in MiAIRR Set 3. In the new spec, read_length and paired_read_length are in the Schema object RawSequenceData as that is where the other paired_* information (e.g., *direction or *filename) is. This is Set 4. Currently, the x-airr tag for *read_length states Set 3, even though this is surrounded by Set 4 data.

Minutes

Meta

  • Date: Fri, 2020-02-14 14:30 UTC
  • Present: Ahmad, Brian, Christian, Florian, John

Follow-up

  • DataRep deferred the decision on renaming organism to species again, will bring it up again in MiniStd Call 2020-03.
  • Object definition cell and related data schema: Discussed at ComRepo call, Sri will go ahead with a schema and API implementation that initially will not support a tabular serialization (as it requires quite some nesting). Information on data schema can be found in Sri's comment of 2020-02-26.
  • CEDAR Templates: Confirmed that templates and their elements can be publicly visible (not requiring login). Also confirmed that CEDAR's version number can be distinct from MiAIRR version (assuming that it clearly labeled).
  • Switching to Github for agendas and minutes: Again no objections, starting test run for this call.

MiAIRR requirement levels

  • This is a combination of issues #310 and #297, which deal with nullable status of field, how to indicate this to users and how to represent it in the data schema.
  • We currently have three requirement levels (adopted from RFC2119) in table200201, where:
    • "present" means that a field exists in a metadata description
    • "NULL" means that a field has a NULL value (as in SQL) or a NULL-like value that does also not provide any information on regarding this field. NULL-like values are currently missing, not applicable and not collected, which were adopted from BioSample attributes
    • MiAIRR field are by default recommended as they are part of a minimal standard and thus MUST be present. Some MiAIRR fields might be required but never optional
level MUST be present CAN be NULL
required yes no
recommended yes yes
optional no yes
  • We agree that only fields that are essential for interpretation of data are required, i.e., MUST NOT be NULL. This is different from the previous interpretation, which stated that all fields of which the information can be expected to be available to the data producer MUST be annotated. Further background in #310 fixed by #319.
  • Issues with the current terms for standard users:
    • "required" does not implicate not being NULL
    • "recommended" is misleading as the field MUST be present
  • Issues with the current representation in the AIRR Schema: OpenAPI knows a required and a nullable property, which potentially creates even more confusion as they have different meaning (nullable only refers to NULL, not to NULL-like) and a different scope (required would not only apply to the MiAIRR part of a field). This is discussed in #297 and will perspectively be fixed via #319.
  • There will most likely never be perfect and 100% self-explanatory terms for the three levels, so documentation will be required. However, the potential confusion with OpenAPI should be resolved.
  • As the terms can be changed later on, we will try to find a reason- able set until the next call. All suggestions welcome.

New Topics

  • read_length field
    • Moved *read_length to Set 4 in #324, merged.
    • Strictly spoken, the addition of the other set: 4 fields already broke compatibility as they are new requirements that were not present in AIRRv1.0. However set: 4 is a dark place for MiAIRR anyhow, as it is just defined as raw data (i.e., not mandatory metadata, so in the real world nothing depends on this).
    • NCBI mapping needs to be updated, documented in #330
    • Format change is could be relevant to CEDAR, who have noted this.
    • Topic can be closed, no follow-up in March until issues arise.

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