Skip to content

Seqcol specification version 0.1.0

Specification version

This specification is in DRAFT form. This is NOT YET AN APPROVED GA4GH specification. This document is formal technical explanation for implementers. See also:

Introduction

Reference sequences are fundamental to genomic analysis. To make their analysis reproducible and efficient, we require tools that can identify, store, retrieve, and compare reference sequences. The primary goal of the Sequence Collections (seqcol) project is to standardize identifiers for collections of sequences. Seqcol can be used to identify genomes, transcriptomes, or proteomes -- anything that can be represented as a collection of sequences. A common example and primary use case of sequence collections is for reference genome, so this documentation sometimes refers to reference genomes for convenience; really, it can be applied to any collection of sequences.

In brief, the project specifies several procedures:

  1. An algorithm for encoding sequence collection identifiers. The GA4GH standard refget sequences specifies a way to compute deterministic sequence identifiers from individual sequences. Seqcol uses refget sequence identifiers and adds functionality to wrap them into collections of sequences. Seqcol also handles sequence attributes, such as their names, lengths, or topologies. Seqcol digests are defined by a hash algorithm, rather than an accession authority, and are thus decentralized and usable for private sequence collections, cases without connection to a central database, or validation of sequence collection content and provenance.
  2. An API describing lookup and comparison of sequence collections. Seqcol specifies a RESTful API to retrieve the sequence collection given a digest. A main use case is to reproduce the exact sequence collection (e.g. reference genome) used for analysis, instead of guessing based on a human-readable identifier. Seqcol also provides a standardized method of comparing the contents of two sequence collections. This comparison function can e.g. be used to determine if analysis results based on different references genomes are compatible.
  3. Recommended ancillary, non-inherent attributes. Finally, the protocol defines several recommended procedures that will improve the compatibility across Seqcol servers, and beyond.

Use cases

Sequence collections represent fundamental concepts; therefore the specification can be used for many use cases. A primary goal is that that seqcol digests could replace or live alongside the human-readable identifiers currently used to identify reference genomes (e.g. "hg38" or "GRCh38"). Reference genomes are an indispensable resource for genome analysis. Such reference data is provided in many versions by various sources. Unfortunately, this reference variation leads to fundamental problems in analysis of reference genomes: computational results are often irreproducible or incompatible because reference genome data they use is either not matching or unidentifiable. These issues are partially caused by our tradition of simple human-readable reference identifiers; this is sub-optimal because such identifiers can refer to references with subtle (or not so subtle) differences, undermining the utility of the identifiers, as is well-known for "hg38" or "GRCh38" monikers. One solution is to use unique identifiers that unambiguously identify a particular assembly, such as those provided by the NCBI Assembly database; however, this approach relies on a central authority, and therefore can not apply to custom genomes. Another weakness of centralized unique identifiers is that they are insufficient to confirm identity, which must also consider the content of the genome. A related problem is determining compatibility among reference genomes. Analytical results based on different genome references may still be integrable, as long as certain conditions about those references are met. However, there are no existing tools or standards to formalize and simplify answering the question of reference genome compatibility.

An earlier standard, the refget sequences protocol, partially addressed this issue for individual sequences, such as a single chromosome, but is not directly applicable to collections of sequences, such as a linear reference genome. Building on refget sequences, sequence collections presents fundamental concepts, and therefore the specification can be used for many use cases. For example, we envision that seqcol identifiers could replace or live alongside the human-readable identifiers currently used to identify reference genomes (e.g. "hg38" or "GRCh38"), which would provide improved reproducibility.

Some other examples of common use cases where the use of seqcol is beneficial include:

  • As a user, I wish to know what sequences are inside a specific collection, so that I can further access those sequences
  • As a user, I want to compare the two sequence collections used by two separate analyses so I can understand how comparable and compatible their resulting data are.
  • As a user, I am interested in a genome sequence collection but want to extract those sequences which compose the chromosomes/karyotype of a genome
  • As a submission system, I want to know what exactly a sequence collection contains so I can validate a data file submission.
  • As a software developer, I want to embed a sequence collection digest in my tool's output so that downstream tools can identify the exact sequence collection that was used
  • I have a chromosome sizes file (a set of lengths and names), and I want to ask whether a given sequence collection is length-compatible with and/or name-compatible with this chromosome sizes file.
  • As a genome browser, I have one sequence collection that the coordinate system displayed, and I want to know if a digest representing the coordinate system of a given BED file is compatible with the genome browser.
  • As a data processor, my input data didn't include information about the reference genome used, and I want to generate the sequence collection digest and attach it so that further processing can benefit from the sequence collection features.

Definitions of key terms

  • Alias: A human-readable identifier used to refer to a sequence collection.
  • Array: An ordered list of elements.
  • Collated: A qualifier applied to a seqcol attribute indicating that the values of the attribute matches 1-to-1 with the sequences in the collection and are represented in the same order.
  • Coordinate system: An ordered list of named sequence lengths, but without actual sequences.
  • Digest: A string resulting from a cryptographic hash function, such as MD5 or SHA512, on input data.
  • Inherent: A qualifier applied to a seqcol attribute indicating that the attribute is part of the definition of the sequence collection and therefore contributes to its digest.
  • Length: The number of characters in a sequence.
  • Seqcol algorithm: The set of instructions used to compute a digest from a sequence collection.
  • Seqcol API: The set of endpoints defined in the retrieval and comparison components of the seqcol protocol.
  • Seqcol digest: A digest for a sequence collection, computed according to the seqcol algorithm.
  • Seqcol protocol: Collectively, the 3 operations outlined in this document, which include: 1. encoding of sequence collections; 2. API describing retrieval and comparison ; and 3. specifications for ancillary recommended attributes.
  • Sequence: Seqcol uses refget sequences to identify actual sequences, so we generally use the term "sequence" in the same way. Refget sequences was designed for nucleotide sequences; however, other sequences could be provided via the same mechanism, e.g., cDNA, CDS, mRNA or proteins. Essentially any ordered list of refget-sequences-valid characters qualifies. Sequence collections also goes further, since sequence collections may contain sequences of non-specified characters, which therefore have a length but no actual sequence content.
  • Sequence digest or refget sequence digest: A digest for a sequence, computed according to the refget sequence protocol.
  • Sequence collection: A representation of 1 or more sequences that is structured according to the sequence collection schema
  • Sequence collection attribute: A property or feature of a sequence collection (e.g. names, lengths, sequences, or topologies).

Seqcol protocol functionality

The seqcol algorithm is based on the refget sequence algorithm for individual sequences and should use refget sequence servers to store the actual sequence data. Seqcol servers therefore provide a lightweight organizational layer on top of refget sequence servers. To be fully compliant with the seqcol protocol an implementation must provide all REQUIRED capabilities as detailed below.

The seqcol protocol defines the following:

  1. Schema - The way an implementation should define the attributes of sequence collections it holds.
  2. Encoding - An algorithm for computing a digest given a sequence collection.
  3. API - A server RESTful API specification for retrieving and comparing sequence collections.
  4. Ancillary attribute management - A specification for organizing non-inherent metadata as part of a sequence collection.

1. Schema: Defining the attributes in the collection

The first step for a Sequence Collections implementation is to define the list of contents, that is, what attributes are allowed in each collection, and which of these affect the digest. The sequence collections standard is flexible with respect to the schema used, so implementations of the standard can use the standard with different schemas, as required by a particular use case. This divides the choice of content from the choice of algorithm, allowing the algorithm to be consistent even in situations where the content is not.

This is an example of a general, minimal schema:

description: "A collection of biological sequences."
type: object
properties:
  lengths:
    type: array
    collated: true
    description: "Number of elements, such as nucleotides or amino acids, in each sequence."
    items:
      type: integer
  names:
    type: array
    collated: true
    description: "Human-readable labels of each sequence (chromosome names)."
    items:
      type: string
  sequences:
    type: array
    collated: true
    items:
      type: string
      description: "Refget sequences v2 identifiers for sequences."
  accessions:
    type: array
    collated: true
    items:
      type: string
      description: "Unique external accessions for the sequences"
required:
  - names
  - lengths
inherent:
  - lengths
  - names
  - sequences

This example schema is the minimal standard schema. We RECOMMEND that all implementations use this as a base schema, adding additional attributes as needed, but without changing the inherent attributes list, because this will keep the identifiers compatible across implementations. Sequence collection objects that follow this basic minimal structure are said to be the canonical seqcol object representation. Adding custom attributes to this schema will not break interoperability. Nevertheless, extending this schema is only RECOMMENDED; implementations are still compliant if using custom schemas with custom inherent attributes.

For more information about community-driven updates to the standard schema, see Footnote F8.

2. Encoding: Computing sequence digests from sequence collections

The encoding function is the algorithm that produces a unique digest for the sequence collection. The input to the function is a set of annotated sequences. This function is generally expected to be provided by local software that operates on a local set of sequences. The steps of the encoding process are:

  • Step 1. Organize the sequence collection data into canonical seqcol object representation and filter the non-inherent attributes.
  • Step 2. Apply RFC-8785 JSON Canonicalization Scheme (JCS) to canonicalize the value associated with each attribute individually.
  • Step 3. Digest each canonicalized attribute value using the GA4GH digest algorithm.
  • Step 4. Apply RFC-8785 JSON Canonicalization Scheme again to canonicalize the JSON of the new seqcol object representation.
  • Step 5. Digest the final canonical representation again using the GA4GH digest algorithm.

Example Python code for computing a seqcol digest can be found in the tutorial for computing seqcol digests. These steps are described in more detail below:

Step 1: Organize the sequence collection data into canonical seqcol object representation.

We first create an object representation of the attributes of the sequence collection. The structure of this object is critical, and is strictly controlled by the seqcol protocol. The sequence collection object MUST first be structured according to the schema definition for the implementation.

Here's an example of a sequence collection organized into the canonical seqcol object representation following the minimal schema example above:

{
  "lengths": [
    248956422,
    133797422,
    135086622
  ],
  "names": [
    "chr1",
    "chr2",
    "chr3"
  ],
  "sequences": [
    "SQ.2648ae1bacce4ec4b6cf337dcae37816",
    "SQ.907112d17fcb73bcab1ed1c72b97ce68",
    "SQ.1511375dc2dd1b633af8cf439ae90cec"
  ]
}

This object would validate against the JSON Schema above. The object is a series of arrays with matching length (3), with the corresponding entries collated such that the first element of each array corresponds to the first element of each other array. For the rationale why this structure was chosen instead of an array of annotated sequences, see Footnote F1. The implementation MUST define its structure in a JSON Schema, such as the example schema defined in step 1. Implementations MAY choose to extend this schema by adding additional attributes. Implmentations MAY also use a schema, but we RECOMMEND the schema extend the base schema defined above. This schema extends vanilla JSON Schema in two ways; first, it provides the collated qualifier. For further details about the rationale behind collated attributes, see Footnote F2. Second, it specifies the inherent qualifier. For further details about the rationale and examples of non-inherent attributes, see Footnote F3. Finally, another detail that may be unintuitive at first is that in the minimal schema, the sequences attribute is optional; for an explanation of why, see Footnote F4.

Filter non-inherent attributes

The inherent section in the seqcol schema is an extension of the basic JSON Schema format that adds specific functionality. Inherent attributes are those that contribute to the digest; non-inherent attributes are not considered when computing the top-level digest. Attributes of a seqcol that are not listed as inherent MUST NOT contribute to the digest; they are therefore excluded from the digest calculation. Therefore, if the canonical seqcol representation includes any non-inherent attributes, these must be removed before proceeding to step 2. In the simple example, there are no non-inherent attributes.

Step 2: Apply RFC-8785 to canonicalize the value associated with each attribute individually.

The RFC-8785 JSON Canonicalization Scheme (JCS) standardizes whitespace, character encodings, and other details that would cause inconsequential variations to yield different digests. For most use cases*, the following Python function suffices:

import json

def canonical_str(item: [list, dict]) -> bytes:
    """Convert a list or dict into a canonicalized UTF8-encoded bytestring representation"""
    return json.dumps(
        item, separators=(",", ":"), ensure_ascii=False, allow_nan=False, sort_keys=True
    ).encode("utf8")

This will turn the values into canonicalized UTF8-encoded bytestring representations of the list objects. Using Python notation, the value of the lengths attribute becomes b'[248956422,133797422,135086622]', the value of the names attribute becomes b'["chr1","chr2","chr3"]', and the value of the sequences attribute becomes 

b'["SQ.2648ae1bacce4ec4b6cf337dcae37816","SQ.907112d17fcb73bcab1ed1c72b97ce68","SQ.1511375dc2dd1b633af8cf439ae90cec"]'

* The above Python function suffices if (1) attribute keys are restricted to ASCII, (2) there are no floating point values, and (3) for all integer values i: -2**63 < i < 2**63

Also, notice that in this process, RFC-8785 is applied only to objects; we assume the sequence digests are computed through an external process (the refget sequences protocol), and are not computed as part of the sequence collection. The refget sequences protocol digests sequence strings without JSON-canonicalization. For more details, see Footnote F5.

Step 3: Digest each canonicalized attribute value using the GA4GH digest algorithm.

Apply the GA4GH digest algorithm to each attribute value. The GA4GH digest algorithm is described in detail in Footnote F6. This converts the value of each attribute in the seqcol into a digest string. Applying this to each value will produce the following structure:

{
  "lengths": "IOlarejnLTmdv3-CqehLpcxAR9yNeR1i",
  "names": "g04lKdxiYtG3dOGeUC5AdKEifw65G0Wp",
  "sequences": "ixJdEJlNBgz5U49vfIUqmq3kD4oOtLpd"
}

Step 4: Apply RFC-8785 again to canonicalize the JSON of the new seqcol object representation.

Here, we repeat step 2, except instead of applying RFC-8785 to each value separately, we apply it to the entire object. This will result in a canonical bytestring representation of the object, shown here using Python notation:

b'{"lengths":"IOlarejnLTmdv3-CqehLpcxAR9yNeR1i","names":"g04lKdxiYtG3dOGeUC5AdKEifw65G0Wp","sequences":"ixJdEJlNBgz5U49vfIUqmq3kD4oOtLpd"}'

Step 5: Digest the final canonical representation again using the GA4GH digest algorithm.

Again using the same approach as in step 3, we now apply the GA4GH digest algorithm to the canonicalized bytestring. The result is the final unique digest for this sequence collection:

wqet7IWbw2j2lmGuoKCaFlYS_R7szczz

Terminology

Because the encoding algorithm is recursive, this leads to a few different ways to represent a sequence collection. We refer to these representations in "levels". The level number represents the number of "lookups" you'd have to do from the "top level" digest. So, we have:

Level 0

Just a plain digest, also known as the "top-level digest". This corresponds to 0 database lookups. Example: 

a6748aa0f6a1e165f871dbed5e54ba62

Level 1

What you'd get when you look up the digest with 1 database lookup (no recursion). We sometimes refer to this as the "array digests" or "attribute digests", because it is made up a digest for each attribute in the sequence collection. Example: 

{
  "lengths": "4925cdbd780a71e332d13145141863c1",
  "names": "ce04be1226e56f48da55b6c130d45b94",
  "sequences": "3b379221b4d6ea26da26cec571e5911c"
}

Level 2

What you'd get with 2 database lookups (1 recursive call). This is the most common representation, and hence, it the level of the canonical seqcol representation. Example:

{
  "lengths": [
    "1216",
    "970",
    "1788"
  ],
  "names": [
    "A",
    "B",
    "C"
  ],
  "sequences": [
    "76f9f3315fa4b831e93c36cd88196480",
    "d5171e863a3d8f832f0559235987b1e5",
    "b9b1baaa7abf206f6b70cf31654172db"
  ]
}

3. API: A server RESTful API specification for retrieving and comparing sequence collections.

The API has 3 top-level endpoints, for 3 functions:

  1. /service-info, for describing information about the service;
  2. /collection, for retrieving sequence collections; and
  3. /comparison, for comparing two sequence collections.

In addition, a RECOMMENDED endpoint at /openapi.json SHOULD provide OpenAPI documentation.

Under these umbrella endpoints are a few more specific sub-endpoints, described in detail below:

3.1 Service info

  • Endpoint: GET /service-info (REQUIRED)
  • Description: The service info endpoint provides information about the service
  • Return value: Must include the Seqcol JSON Schema that is used by this server

The /service-info endpoint should follow the GA4GH-wide specification for service info for general description of the service. Then, it should also add a few specific pieces of information under a seqcol property: - schema: MUST return the JSON Schema implemented by the server.

The service-info JSON-schema document

The schema attribute of service-info return value MUST provide a single schema, this MUST include all possible attributes your service may provide. In other words, you cannot have a collection with an attribute that is not defined in your schema.

We RECOMMEND the schema only define terms actually used in at least one collection served; however, it is allowed for the schema to contain extra terms that are not used in any collections in the server.

We RECOMMEND your schema use property-level refs to point to terms defined by a central, approved seqcol schema. However, it is also allowed for the schema to embed all definitions locally. The central, approved seqcol schema will be made available as the spec is finalized.

For example, here's a JSON schema that uses a ref to reference the approved seqcol schema:

description: "A collection of biological sequences."
type: object
"$id": "https://example.com/sequence_collection",  # URI to main seqcol definition
properties:
  lengths:
    "$ref": "/lengths"
  names:
    "$ref": "/names"
  sequences:
    "$ref": "/sequences"
required:
  - names
  - lengths
inherent:
  - lengths
  - names
  - sequences

3.2 Collection

  • Endpoint: GET /collection/:digest?level=:level (REQUIRED)
  • Description: Retrieves original sequence collection from a database, keyed by the unique top-level digest. Here :digest is the seqcol digest computed above. The level corresponds to the "expansion level" of the returned sequence collection returned. The default is ?level=2, which returns the canonical structure.
  • Return value: The sequence collection identified by the :digest variable. The structure of the data MUST be modulated by the :level query parameter. Specifying ?level=2 returns the canonical structure, and ?level=1 returns the collection with digested attributes.

Non-inherent attributes MUST be stored and returned by the collection endpoint alongside inherent attributes.

3.3 Comparison

  • Endpoint 1: GET /comparison/:digest1/:digest2 (RECOMMENDED) Two-digest comparison
  • Endpoint 2: POST /comparison/:digest1 (RECOMMENDED) One-digest POST comparison
  • Description: The comparison function specifies an API endpoint that allows a user to compare two sequence collections. The collections are provided either as two digests (the GET endpoint) or as one digest representing a database collection, and one local user-provided collection provided via POST. For the POST endpoint variant, the user-provided local collection should be provided as a level 2 representation (AKA the canonical seqcol representation) in the BODY of the POST request.
  • Return value: The output is an assessment of compatibility between those sequence collections. If implemented, both variants of the /comparison endpoint must MUST return an object in JSON format with these 3 keys: digests, arrays, and elements, as described below (see also an example after the descriptions):
    • digests: an object with 2 elements, with keys a and b, and values either the level 0 seqcol digests for the compared collections, or null (undefined). The value MUST be the level 0 seqcol digest for any digests provided by the user for the comparison. However, it is OPTIONAL for the server to provide digests if the user provided the sequence collection contents, rather than a digest. In this case, the server MAY compute and return the level 0 seqcol digest, or it MAY return null (undefined) in this element for any corresponding sequence collection.
    • attributes: an object with 3 elements, with keys a_only, b_only, and a_and_b. The value of each element is a list of array names corresponding to arrays only present in a, only present in b, or present in both a and b.
    • array_elements: An object with 4 elements: a_count, b_count, a_and_b_count, and a_and_b_same_order. The 3 attributes with _count are objects with names corresponding to each array present in the collection, or in both collections (for a_and_b_count), with values as the number of elements present either in one collection, or in both collections for the given array. a_and_b_same_order is also an object with names corresponding to arrays, and the values a boolean following the same-order specification below.

Example /comparison return value: 

{
  "digests": {
    "a": "514c871928a74885ce981faa61ccbb1a",
    "b": "c345e091cce0b1df78bfc124b03fba1c"
  },
  "attributes": {
    "a_only": [],
    "b_only": [],
    "a_and_b": [
      "lengths",
      "names",
      "sequences"
    ]
  },
  "array_elements": {
    "a_count": {
      "lengths": 195,
      "names": 195,
      "sequences: 195
    },
    "b_count": {
      "lengths": 25,
      "names": 25,
      "sequences: 25
    }
    "a_and_b_count": {
      "lengths": 25,
      "names": 25,
      "sequences": 0
    },
    "a_and_b_same_order": {
      "lengths": false,
      "names": false,
      "sequences": null
    }
  }
}

Same-order specification

The comparison return includes an a_and_b_same_order boolean value for each array that is present in both collections. The defined value of this attribute is:

  • undefined (null) if there are fewer than 2 overlapping elements
  • undefined (null) if there are unbalanced duplicates present (see definition below)
  • true if all matching elements are in the same order in the two arrays
  • false otherwise.

An unbalanced duplicate is used in contrast with a balanced duplicate. Balanced means the duplicates are the same in both arrays. When the duplicates are balanced, order is still defined; but if duplicates are unbalanced, this means an array has duplicates not present in the other, and in that case, order is not defined.

Interpreting the result of the compare function

The output of the comparison function provides information-rich feedback about the two collections. These details can be used to make a variety of inferences comparing two collections, but it can take some thought to interpret. For more details about how to interpret the results of the comparison function to determine different types of compatibility, please see the howto guide on comparing sequencing collections.

3.4 OpenAPI documentation

In addition to the primary top-level endpoints, it is RECOMMENDED that the service provide /openapi.json, an OpenAPI-compatible description of the endpoints.

In Section 1: Encoding, we distinguished between inherent and non-inherent attributes. Non-inherent attributes provide a standardized way for implementations to store and serve additional, third-party attributes that do not contribute to the digest. As long as separate implementations keep such information in non-inherent attributes, the digests will remain compatible. Furthermore, the structure for how such non-inherent metadata is retrieved will be standardized. Here, we specify standardized, useful non-inherent attributes that we recommend.

The sorted_name_length_pairs attribute is a non-inherent attribute of a sequence collection with a formal definition, provided here. When digested, this attribute provides a digest for an order-invariant coordinate system for a sequence collection. Because it is non-inherent, it does not affect the identity (digest) of the collection. It is created deterministically from the names and lengths attributes in the collection; it does not depend on the actual sequence content, so it is consistent across two collections with different sequence content if they have the same names and lengths, which are correctly collated, but with pairs not necessarily in the same order. This attribute is RECOMMENDED to allow unified genome browser visualization of data defined on different reference sequence collections. For more rationale and use cases of sorted_name_length_pairs, see Footnote F7.

Algorithm:

  1. Lump together each name-length pair from the primary collated names and lengths into an object, like {"length":123,"name":"chr1"}.
  2. Canonicalize JSON according to the seqcol spec (using RFC-8785).
  3. Digest each name-length pair string individually.
  4. Sort the digests lexicographically.
  5. Add as a non-inherent, non-collated attribute to the sequence collection object.

4.2 The sorted_sequences attribute (OPTIONAL)

The sorted_sequences attribute is a non-inherent attribute of a sequence collection, with a formal definition. Providing this attribute is OPTIONAL. When digested, this attribute provides a digest representing an order-invariant set of unnamed sequences. It provides a way to compare two sequence collections to see if their sequence content is identical, but just in a different order. Such a comparison can, of course, be made by the comparison function, so why might you want to include this attribute as well? Simply that for some large-scale use cases, comparing the sequence content without considering order is something that needs to be done repeatedly and for a huge number of collections. In these cases, using the comparison function could be computationally prohibitive. This digest allows the comparison to be pre-computed, and more easily compared.

Algorithm:

  1. Take the array of the sequences attribute (an array of sequence digests) and sort it lexicographically.
  2. Canonicalize the resulting array (using RFC-8785).
  3. Add to the sequence collection object as the sorted_sequences attribute, which is non-inherent and non-collated.

Footnotes

F1. Why use an array-oriented structure instead of a sequence-oriented structure?

In the canonical seqcol object structure, we first organize the sequence collection into what we called an "array-oriented" data structure, which is a list of collated arrays (names, lengths, sequences, etc.). An alternative we considered was a "sequence-oriented" structure, which would group each sequence with some attributes, like {name, length, sequence}, and structure the collection as an array of such objects. While the latter is intuitive, as it captures each sequence object with some accompanying attributes as independent entities, there are several reasons we settled on the array-oriented structure instead:

  1. Flexibility and backwards compatibility of sequence attributes. What happens for an implementation that adds a new attribute? For example, if an implementation adds a topology attribute to the sequences, in the sequence-oriented structure, this would alter the sequence objects and thereby change their digests. In the array-based structure, since we digest the arrays individually, the digests of the other arrays are not changed. Thus, the array-oriented structure emphasizes flexibility of attributes, where the sequence-oriented structure would emphasize flexibility of sequences. In other words, the array-based structure makes it straightforward to mix-and-match attributes of the collection. Because each attribute is independent and not integrated into individual sequence objects, it is simpler to select and build subsets and permutations of attributes. We reasoned that flexibility of attributes was desirable.

  2. Conciseness. Sequence collections may be used for tens of thousands or even millions of sequences. For example, a transcriptome may contain a million transcripts. The array-oriented data structure is a more concise representation for digesting collections with many elements because the attribute names are specified once per collection instead of once per element. Furthermore, the level 1 representation of the sequence collection is more concise for large collections, since we only need one digest per attribute, rather than one digest per sequence.

  3. Utility of intermediate digests. The array-oriented approach provides useful intermediate digests for each attribute. This digest can be used to test for matching sets of sequences, or matching coordinate systems, using the individual component digests. With a sequence-oriented framework, this would require traversing down a layer deeper, to the individual elements, to establish identity of individual components. The alternative advantage we would have from a sequence-oriented structure would be identifiers for annotated sequences. We can gain the advantages of these digests through adding a custom non-inherent, but collated attribute that calculates a unique digest for each element based on the selected attributes of interest, e.g. named_sequences (digest of e.g. b'{"name":"chr1","sequence":"SQ.2648ae1bacce4ec4b6cf337dcae37816"}').

See ADR on 2021-06-30 on array-oriented structure

F2. Collated attributes

In JSON Schema, there are 2 ways to qualify properties: 1) a local qualifier, using a key under a property; or 2) an object-level qualifier, which is specified with a keyed list of properties up one level. For example, you annotate a property's type with a local qualifier, underneath the property, like this:

properties:
  names:
    type: array

However, you specify that a property is required by adding it to an object-level required list that's parallel to the properties keyword:

properties:
  names:
    type: array
required:
  - names

In sequence collections, we chose to define collated as a local qualifier. Local qualifiers fit better for qualifiers independent of the object as a whole. They are qualities of a property that persist if the property were moved onto a different object. For example, the type of an attribute is consistent, regardless of what object that attribute were defined on. In contrast, object-level qualifier lists fit better for qualifiers that depend on the object as a whole. They are qualities of a property that depend on the object context in which the property is defined. For example, the required modifier is not really meaningful except in the context of the object as a whole. A particular property could be required for one object type, but not for another, and it's really the object that induces the requirement, not the property itself.

We reasoned that inherent, like required, describes the role of an attribute in the context of the whole object; an attribute that is inherent to one type of object need not be inherent to another. Therefore, it makes sense to treat this concept the same way JSON schema treats required. In contrast, the idea of collated describes a property independently: Whether an attribute is collated is part of the definition of the attribute; if the attribute were moved to a different object, it would still be collated.

F3. Details of inherent and non-inherent attributes

The specification in section 1, Encoding, described how to structure a sequence collection and then apply an algorithm to compute a digest for it. What if you have ancillary information that goes with a collection, but shouldn't contribute to the digest? We have found a lot of useful use cases for information that should go along with a seqcol, but should not contribute to the identity of that seqcol. This is a useful construct as it allows us to include information in a collection that does not affect the digest that is computed for that collection. One simple example is the "author" or "uploader" of a reference sequence; this is useful information to store alongside this collection, but we wouldn't want the same collection with two different authors to have a different digest! Seqcol refers to these as non-inherent attributes, meaning they are not part of the core identity of the sequence collection. Non-inherent attributes are defined in the seqcol schema, but excluded from the inherent list.

See: ADR on 2023-03-22 regarding inherent attributes

F4. Sequence collections without sequences

Typically, we think of a sequence collection as consisting of real sequences, but in fact, sequence collections can also be used to specify collections where the actual sequence content is irrelevant. Since this concept can be a bit abstract for those not familiar, we'll try here to explain the rationale and benefit of this. First, consider that in a sequence comparison, for some use cases, we may be primarily concerned only with the length of the sequence, and not the actual sequence of characters. For example, BED files provide start and end coordinates of genomic regions of interest, which are defined on a particular sequence. On the surface, it seems that two genomic regions are only comparable if they are defined on the same sequence. However, this not strictly true; in fact, really, as long as the underlying sequences are homologous, and the position in one sequence references an equivalent position in the other, then it makes sense to compare the coordinates. In other words, even if the underlying sequences aren't exactly the same, as long as they represent something equivalent, then the coordinates can be compared. A prerequisite for this is that the lengths of the sequence must match; it wouldn't make sense to compare position 5,673 on a sequence of length 8,000 against the same position on a sequence of length 9,000 because those positions don't clearly represent the same thing; but if the sequences have the same length and represent a homology statement, then it may be meaningful to compare the positions.

We realized that we could gain a lot of power from the seqcol comparison function by comparing just the name and length vectors, which typically correspond to a coordinate system. Thus, actual sequence content is optional for sequence collections. We still think it's correct to refer to a sequence-content-less sequence collection as a "sequence collection" -- because it is still an abstract concept that is representing a collection of sequences: we know their names, and their lengths, we just don't care about the actual characters in the sequence in this case. Thus, we can think of these as a sequence collection without sequence characters.

An example of a canonical representation (level 2) of a sequence collection with unspecified sequences would be:

{
  "lengths": [
    "1216",
    "970",
    "1788"
  ],
  "names": [
    "A",
    "B",
    "C"
  ]
}

F5. RFC-8785 does not apply to refget sequences

A note to clarify potential confusion with RFC-8785. While the sequence collection specification determines that RFC-8785 will be used to canonicalize the JSON before digesting, this is specific to sequence collections, it does not apply to the original refget sequences protocol. According to the sequences protocol, sequences are digested as un-quoted strings. If RFC-8785 were applied at the level of individual sequences, they would be quoted to become valid JSON, which would change the digest. Since the sequences protocol predated the sequence collections protocol, it did not use RFC-8785; and anyway, the sequences are just primitive types so a canonicalization scheme doesn't add anything. This leads to the slight confusion that RFC-8785 canonicalization is only applied to the objects in the sequence collections, and not to the primitives when the underlying sequences are digested.

F6. The GA4GH digest algorithm

The GA4GH digest algorithm, sha512t24u, was created as part of the Variation Representation Specification standard. This procedure is described as (Hart et al. 2020):

  • performing a SHA-512 digest on a binary blob of data
  • truncate the resulting digest to 24 bytes
  • encodes the 24 bytes using base64url (RFC 4648) resulting in a 32 character string

In Python, the digest can be computed with this function:

import base64
import hashlib

def sha512t24u_digest(seq: bytes) -> str:
    """ GA4GH digest function """
    offset = 24
    digest = hashlib.sha512(seq).digest()
    tdigest_b64us = base64.urlsafe_b64encode(digest[:offset])
    return tdigest_b64us.decode("ascii")

See: ADR from 2023-01-25 on digest algorithm

F7. Use cases for the sorted_name_length_pairs non-inherent attribute

One motivation for this attribute comes from genome browsers, which may display genomic loci of interest (e.g. BED files). The genome browser should only show BED files if they annotate the same coordinate system as the reference genome. This is looser than strict identity, since we don't really care what the underlying sequence characters are, as long as the positions are comparable. We also don't care about the order of the sequences. Instead, we need them to match level 1 digest of the sorted_name_length_pairs attribute. Thus, to assert that a BED file can be viewed for a particular genome, we compare the sorted_name_length_pairs digest of our reference genome with the sequence collection used to generate the file. There are only two possibilities for compatibility: 1) If the digests are equal, then the data file is directly compatible; 2) If not, we must check the comparison endpoint to see whether the sorted_name_length_pairs attribute of the sequence collection is a direct subset of the same array in the sequence collection attached to the genome browser instance. If so, the data file is still compatible.

For efficiency, if the second case is true, we may cache the sorted_name_length_pairs digest in a list of known compatible reference genomes. In practice, this list will be short. Thus, in a production setting, the full compatibility check can be reduced to a lookup into a short, pre-generated list of sorted_name_length_pairs digests.

See: ADR from 2023-07-12 on sorted name-length pairs

F8. Adding new schema attributes

A strength of the seqcol standard is that the schema definition can be modified for particular use cases, for example, by adding new attributes into a sequence collection. This will allow different communities to use the standard without necessarily needing to subscribe to identical schemas, allowing the standard to be more generally useful. However, if communities define too many custom attributes, this leads to the possibility of fragmentation. For example, two implementations may start using the same attribute name to refer to different concepts. While the attributes would still be formally defined in the respective schemas provided by each implementation, calling different concepts by the same name would come at the cost of interoperability. Therefore, the standard will also include in the schema a list of formally defined attributes, to encourage interoperability of these attributes. The goal is not to include all possible attributes in the schema, but just those likely to be used repeatedly, to encourage interoperable use of those attribute names. An implementation may propose a new attribute to be added to this extended schema by raising an issue on the GitHub repository. The proposed attributes and definition can then be approved through discussion during the refget working group calls and ultimately added to the approved extended seqcol schema. These GitHub issues should be created with the label 'schema-term'. You can follow these issues (or raise your own) at https://github.com/ga4gh/seqcol-spec/issues?q=is%3Aissue+label%3Aschema-term+.