sdrf-cellline

name: sdrf:cellline description: Use when the user needs to look up cell line metadata or enrich an SDRF with cell-line-derived characteristics (organism, disease, sex, sampling site, ancestry, age). Triggers on cell line names (HeLa, MCF-7, A549, …), Cellosaurus accessions (CVCL_XXXX), or "annotate cell line" requests. user-invocable: true argument-hint: "[cell line name | CVCL_XXXX | path/to/file.sdrf.tsv]"

SDRF Cell Line Annotation

You are translating cell line identity into the SDRF columns required by the cell-lines template. The source of truth is Cellosaurus (SIB / Expasy) — it is not hosted on EBI OLS, so this skill queries Cellosaurus directly. OLS is still used for the target ontologies the SDRF columns reference (NCBITaxon, MONDO, UBERON, HANCESTRO, CLO/BTO/EFO). This skill encodes the rules for the translation — it does not ship a local database.

Cellosaurus access

Use the REST API by default. Drop to the bulk file only when the user asks for offline mode or needs to enrich many SDRFs in one pass.

When to Use

• A single cell line lookup ("What is HeLa?" / "Look up CVCL_0030").
• Enriching an SDRF where characteristics[cell line] is filled but the Cellosaurus-derivable columns (organism, disease, sampling site, sex, ancestry, age, developmental stage, cellosaurus accession/name) are blank, generic, or inconsistent.
• Resolving ambiguous cell line names raised by /sdrf:annotate, /sdrf:validate, or /sdrf:fix.

For pure ontology-term lookup unrelated to cell lines, use /sdrf:terms.

Step 0: Identify the cell-lines template requirements

Always read the template first — column names, requirement levels, and target ontologies must come from the spec, never from memory.

Read: spec/sdrf-proteomics/sdrf-templates/cell-lines/{version}/cell-lines.yaml

Required columns supplied by Cellosaurus (most current spec):

Flat-file field codes are the two-letter codes in cellosaurus.txt (ID, AC, SY, OX, DI, DR, SX, AG, …); JSON field names from the REST API are listed in Step 2a.

The cell-lines template also requires an organism layer (human / vertebrates / invertebrates), which contributes characteristics[organism]. Take the species from Cellosaurus's OX line (taxon ID) and verify against the organism template's NCBITaxon column.

Step 1: Normalize the input

Cell line names in the wild are messy. Apply this pipeline before any lookup:

1. Strip enclosing punctuation/quotes/brackets. "['HeLa']" → HeLa. (The /sdrf:fix artifact rule handles this; rerun if dirty.)
2. Trim whitespace at both ends.
3. Recognize an accession directly. Pattern ^CVCL_[A-Z0-9]{4,}$ → skip name lookup, fetch the accession.
4. Build a normalized key for matching only (do not store this): lower(input) with [\s\-_]+ collapsed away. So HeLa-S3, hela s3, HELA_S3, hela.s3 all key to helas3.
5. Reject obvious non-cell-lines. Reserved words (not available, not applicable), tissue names without a clonal identifier, and primary tissue codes are not cell lines — return early and tell the user.

Step 2: Look up Cellosaurus

2a. Online (default)

By accession (CVCL_XXXX):
  GET https://api.cellosaurus.org/cell-line/<CVCL_id>?format=json

By name (exact, then synonyms):
  GET https://api.cellosaurus.org/search/cell-line?q=id:<name>&format=json
  GET https://api.cellosaurus.org/search/cell-line?q=sy:<name>&format=json

By normalized key (last resort, broad search):
  GET https://api.cellosaurus.org/search/cell-line?q=<normalized>&format=json

A JSON response carries a Cellosaurus.cell-line-list array. For each hit, read identifier (recommended name), accession, name-list (synonyms with type=synonym), species-list (NCBI taxon), disease-list (NCIt / ORDO xrefs), derived-from, category, sex, age, and xref-list (which includes CLO / BTO / EFO cross-references — see Step 4.1).

If the API is unreachable (network blocked, rate-limited), fall back to 2b.

2b. Offline (bulk file)

If the user has downloaded the bulk release, point them to one of:

~/cellosaurus.txt   # flat-file format, grep-friendly
~/cellosaurus.obo   # OBO, parsable with standard tools
~/cellosaurus.xml   # XML, machine-readable

Download command (only suggest if the user has no copy):

curl -sSLO https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt

For ad-hoc lookups in the flat file:

# By accession
awk -v RS='//' '/AC   CVCL_0030/' cellosaurus.txt
# By name (case-insensitive, exact line match on ID or SY)
awk -v RS='//' 'BEGIN{IGNORECASE=1} /^ID   HeLa$|^SY[^\n]*\bHeLa\b/' cellosaurus.txt

Never paste large excerpts of the file into the SDRF — extract only the fields needed for Step 4.

Step 3: Disambiguation rules

When Step 2 yields more than one candidate, pick in this order:

1. Exact accession match wins outright.
2. Exact recommended-name match on identifier (case-sensitive).
3. Exact synonym match in name-list entries with type=synonym.
4. Parent-line preference: if both a parent (HeLa, CVCL_0030) and a subclone (HeLa-S3, CVCL_0058) match, prefer the parent only when the user input has no qualifier. If the input contains a digit, letter suffix, or - segment (e.g. HeLa-S3, K562/ADR), prefer the subclone.
5. Hybrid / hybridoma / patient-derived lines (Cellosaurus category Hybridoma, Patient-derived xenograft cell line) are valid hits — flag them in the report so reviewers know the donor metadata semantics differ.
6. Multiple plausible canonical hits → do not guess. Present the top 3 to the user with accession + species + disease and ask which one. Common ambiguous queries: 293, SK, HCT, HEK, T-47.

If nothing matches:

• Suggest the user check spelling, then offer /sdrf:terms cell line "<name>" for a broader CLO/BTO/EFO search.
• Set characteristics[cell line] to the user's input verbatim and the rest of the cell-line columns to not available (never N/A, never unknown).

Step 4: Translate Cellosaurus → SDRF

For each matched cell line, fill columns from these rules. CVCL accessions are verified against Cellosaurus (Step 2). Every other accession written to the SDRF (NCBITaxon:*, MONDO:*, UBERON:*, HANCESTRO:*, EFO:*) must be verified via OLS before writing.

4.1 Direct fields

4.2 Organism (cross-template)

Cellosaurus OX gives NCBI_TaxID=<n>; ! <species>. Translate:

• Look up NCBITaxon:<n> via OLS. Use the canonical label (e.g. Homo sapiens, not human) for characteristics[organism].
• If species ≠ what the chosen organism layer template covers (human = 9606, vertebrates = non-human vertebrates, invertebrates = the rest), warn: the user picked the wrong organism template.

4.3 Disease (NCIt → MONDO/EFO)

Cellosaurus DI lines reference NCIt (e.g. NCIt; C27677; …). The SDRF disease column wants MONDO / EFO / DOID / PATO (per TERMS.tsv).

Translation steps:

1. Get the NCIt term via OLS: searchClasses(query="<NCIt id>", ontologyId="ncit").
2. Read its cross_references. Prefer in this order: MONDO > EFO > DOID.
3. If no cross-reference exists, search the NCIt label text in MONDO: searchClasses(query="<label>", ontologyId="mondo"). Choose the closest match by exact label, then by synonym.
4. If the donor was healthy (Cellosaurus DI absent or "Normal tissue"), set characteristics[disease] to normal (per the cell-lines template guidance), not "not applicable".
5. Multiple DI lines → use the most specific one; record the others in comment[disease history] only if the template extends that column.

4.4 Sampling site / cell type

Cellosaurus DR and SX describe origin tissue/cell type.

• characteristics[sampling site] ← UBERON term for the tissue. Use OLS searchClasses(query="<site>", ontologyId="uberon"). Fall back to BTO if UBERON has no exact match.
• If the source is a fluid (blood, plasma, ascites), use the UBERON term for the fluid; do not invent a tissue.
• If origin is "embryonic kidney" or "fetal liver", set characteristics[developmental stage] to embryonic / fetal (EFO terms) alongside the sampling site.

4.5 Sex

Cellosaurus SX field (Sex: Female | Male | Mixed sex | Sex unspecified):

• Female → female
• Male → male
• Mixed sex → mixed
• Sex unspecified / absent → not available

Lowercase always. Never M/F. The cell-lines template inherits characteristics[sex] from the organism layer.

4.6 Ancestry

Cellosaurus OX may include population annotations (e.g. ! European).

• Map to HANCESTRO via OLS. Common: European → HANCESTRO:0005, African → HANCESTRO:0010, East Asian → HANCESTRO:0009.
• If absent, set characteristics[ancestry category] to not available. Do not infer ancestry from the disease or organism part.

4.7 Age / developmental stage

Cellosaurus AG (donor age) and category give:

• Numeric age (e.g. 31Y) → characteristics[age] formatted as <n>Y / <n>M / <n>W / <n>D (SDRF rule). Reject free text like 31 years — fix it.
• Age range (30Y-35Y) → keep the range, hyphen only.
• Adult, Embryo, Fetus, Newborn → characteristics[developmental stage] using the EFO term, not characteristics[age].

4.8 Columns Cellosaurus does NOT provide

The cell-lines template also defines passage number, biorepository, cell line authentication, culture medium, and sample storage temperature. Cellosaurus has no values for these — they are study-specific. Either:

• Take them from the paper / PRIDE submission via /sdrf:annotate, or
• Set them to not available if the paper does not state them.

Step 5: Bulk enrichment of an SDRF

When the input is a .sdrf.tsv file:

1. Read the file. Detect the cell-line column (header characteristics[cell line], case-insensitive trim).
2. Build the unique set of cell-line values (skip reserved words).
3. Run Steps 1–4 once per unique value — do not re-query for duplicates.
4. For each row, fill empty / not available Cellosaurus-derivable columns. Do not overwrite existing values that disagree with Cellosaurus — instead, surface them as conflicts and ask the user, exactly the way /sdrf:review does.
5. If the SDRF lacks a needed column entirely (e.g. characteristics[cellosaurus accession]), insert it adjacent to characteristics[cell line] and re-emit the full TSV.
6. Produce a short report:

Cell line annotation report
  Unique cell lines: 4
    HeLa            → CVCL_0030  (matched: exact)
    MCF-7           → CVCL_0031  (matched: synonym "MCF7")
    HEK 293T        → CVCL_0063  (matched: normalized "hek293t")
    in-house ABC-1  → unmatched  (kept verbatim, others = not available)
  Conflicts: 0
  Filled cells: 18 across 12 rows

Step 6: Validate

After enrichment, validate against the combined templates:

parse_sdrf validate-sdrf \
  --sdrf_file <enriched>.sdrf.tsv \
  --template cell-lines

Then run /sdrf:validate for ontology-level checks. Round-trip rules:

• CVCL_* accessions must resolve via the Cellosaurus REST API (/cell-line/<CVCL_id>).
• NCBITaxon:*, MONDO:*, UBERON:*, HANCESTRO:*, EFO:* must resolve via OLS.

Important rules

• Never invent accessions. Every accession written must come from a real Cellosaurus or OLS hit in this session. If unsure, write not available.
• Never overwrite curator-supplied values silently. Conflicts are flagged.
• Never commit a local cell-line database to this repo. Cell-line metadata is fetched live from Cellosaurus (REST or freshly downloaded bulk file) so it tracks upstream updates — the bulk file, if used, is treated as a transient cache, not source code.
• Reserved words: not available for unknown, not applicable for inapplicable. Never N/A, NA, unknown, blank.
• Preserve case in cellosaurus name exactly as Cellosaurus returns it (it is a proper noun). Free-text cell line may be the lab's preferred alias.