tooluniverse 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/cellosaurus_tool.py

@@ -0,0 +1,1332 @@
+import os
+import re
+import requests
+from typing import Any, Dict, List, Tuple
+from difflib import SequenceMatcher
+
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+
+@register_tool("CellosaurusSearchTool")
+class CellosaurusSearchTool(BaseTool):
+    """
+    Tool to search Cellosaurus cell lines using the official API.
+    """
+
+    def __init__(self, tool_config, base_url="https://api.cellosaurus.org"):
+        super().__init__(tool_config)
+        self.base_url = base_url
+        self.timeout_seconds = int(os.environ.get("CELLOSAURUS_TIMEOUT", "30"))
+
+    def run(self, arguments):
+        q = arguments.get("q")
+        offset = arguments.get("offset", 0)
+        size = arguments.get("size", 20)
+
+        if not q:
+            return {"error": "`q` parameter is required."}
+
+        return self._search_cell_lines(q, offset, size)
+
+    def _search_cell_lines(self, query, offset, size):
+        """
+        Search Cellosaurus cell lines using the /search/cell-line endpoint.
+        """
+        try:
+            params = {"q": query.strip(), "offset": offset, "size": size}
+
+            url = f"{self.base_url}/search/cell-line"
+            headers = {"Accept": "application/json"}
+            resp = requests.get(
+                url,
+                params=params,
+                headers=headers,
+                timeout=self.timeout_seconds,
+            )
+            resp.raise_for_status()
+            data = resp.json()
+
+            # Extract cell lines from the API response structure
+            cell_lines = []
+            total_count = 0
+
+            if isinstance(data, dict) and "Cellosaurus" in data:
+                cellosaurus_data = data["Cellosaurus"]
+                if "cell-line-list" in cellosaurus_data:
+                    cell_lines = cellosaurus_data["cell-line-list"]
+                    total_count = len(cell_lines)
+
+            return {
+                "success": True,
+                "results": {
+                    "cell_lines": cell_lines,
+                    "total": total_count,
+                    "offset": offset,
+                    "size": size,
+                },
+                "query": query.strip(),
+            }
+        except requests.HTTPError as http_err:
+            status = getattr(http_err.response, "status_code", None)
+            return {"error": f"HTTP {status}: {http_err}"}
+        except Exception as e:
+            return {"error": str(e)}
+
+
+@register_tool("CellosaurusQueryConverterTool")
+class CellosaurusQueryConverterTool(BaseTool):
+    """
+    Tool to convert natural language queries to Solr syntax for
+    Cellosaurus API.
+    """
+
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+
+        # Complete Cellosaurus field definitions from official API
+        # documentation
+        # https://api.cellosaurus.org/api-fields
+        self.cellosaurus_fields = {
+            "id": {
+                "short_name": "-",
+                "description": (
+                    "Recommended name. Most frequently the name of the cell "
+                    "line as provided in the original publication."
+                ),
+                "keywords": [
+                    "name",
+                    "cell line",
+                    "cellline",
+                    "recommended",
+                    "publication",
+                ],
+            },
+            "sy": {
+                "short_name": "-",
+                "description": (
+                    "List of synonyms. We try to list all the different "
+                    "synonyms for the cell line, including alternative use of "
+                    "lower and upper cases characters. Misspellings are not "
+                    'included in synonyms (see the "misspelling" tag).'
+                ),
+                "keywords": [
+                    "synonym",
+                    "synonyms",
+                    "alias",
+                    "alternative",
+                    "different names",
+                ],
+            },
+            "idsy": {
+                "short_name": "-",
+                "description": (
+                    "Recommended name with all its synonyms. Concatenation of "
+                    "ID and SY."
+                ),
+                "keywords": [
+                    "name",
+                    "synonyms",
+                    "combined",
+                    "concatenation",
+                ],
+            },
+            "ac": {
+                "short_name": "-",
+                "description": (
+                    "Primary accession. It is the unique identifier of the "
+                    "cell line. It is normally stable across Cellosaurus "
+                    "versions but when two entries are merged, one of the two "
+                    "accessions stays primary while the second one becomes "
+                    "secondary (see ACAS)"
+                ),
+                "keywords": [
+                    "accession",
+                    "primary",
+                    "identifier",
+                    "unique",
+                    "stable",
+                ],
+            },
+            "acas": {
+                "short_name": "-",
+                "description": (
+                    "Primary and secondary accession. Secondary accession are "
+                    "former primary accession kept here to ensure the access "
+                    "to a cell line via old identifiers."
+                ),
+                "keywords": [
+                    "accession",
+                    "primary",
+                    "secondary",
+                    "former",
+                    "old identifiers",
+                ],
+            },
+            "dr": {
+                "short_name": "-",
+                "description": (
+                    "Cross-references to external resources: cell catalogs, "
+                    "databases, resources listing cell lines as samples or to "
+                    "ontologies. A cross-reference has two parts: the short "
+                    "name of the resource (i.e. CCLE) and an identifier used "
+                    "to locate a particular entry of the resource related to "
+                    "the cell line. For a formal description of all the "
+                    "resources referred to in Cellosaurus, see here ."
+                ),
+                "keywords": [
+                    "cross-reference",
+                    "external",
+                    "catalog",
+                    "database",
+                    "atcc",
+                    "dsmz",
+                    "ccle",
+                    "ecacc",
+                ],
+            },
+            "ref": {
+                "short_name": "-",
+                "description": (
+                    "Publication references. Mostly publications describing "
+                    "the establishment of a cell line or its "
+                    "characterization. Can be journal articles, book "
+                    "chapters, patents and theses. Contains the "
+                    "cross-reference of the publication, its title, authors "
+                    "(or group/consortium) and citation elements."
+                ),
+                "keywords": [
+                    "reference",
+                    "publication",
+                    "paper",
+                    "article",
+                    "journal",
+                    "book",
+                    "patent",
+                    "thesis",
+                ],
+            },
+            "rx": {
+                "short_name": "-",
+                "description": (
+                    "Publication cross-reference. A unique identifier "
+                    "allowing access the publication online. The "
+                    "cross-reference has two parts: the shortname of the "
+                    "online resource (i.e. PubMed, DOI, PMCID, CLPUB) "
+                    "and an identifier used to locate the particular "
+                    "publication related to the cell line. For a formal "
+                    "description of all the resources referred to in "
+                    "Cellosaurus, see here ."
+                ),
+                "keywords": [
+                    "cross-reference",
+                    "online",
+                    "pubmed",
+                    "doi",
+                    "pmcid",
+                    "clpub",
+                    "patent",
+                    "identifier",
+                ],
+            },
+            "ra": {
+                "short_name": "-",
+                "description": (
+                    "Publication authors. List of authors of a publication "
+                    "referenced in a cell line entry."
+                ),
+                "keywords": [
+                    "author",
+                    "authors",
+                    "written by",
+                    "publication",
+                ],
+            },
+            "rt": {
+                "short_name": "-",
+                "description": (
+                    "Publication title. Title of a publication referenced in "
+                    "cell line entry."
+                ),
+                "keywords": ["title", "paper", "article", "publication"],
+            },
+            "rl": {
+                "short_name": "-",
+                "description": (
+                    "Publication citation elements. Citation elements of a "
+                    "publication referenced in a cell line entry."
+                ),
+                "keywords": ["citation", "cite", "reference", "elements"],
+            },
+            "ww": {
+                "short_name": "-",
+                "description": "Web page related to the cell line",
+                "keywords": ["website", "web page", "homepage", "url"],
+            },
+            "anc": {
+                "short_name": "genome-ancestry",
+                "description": (
+                    "Estimated ethnic ancestry of the donor of a human cell "
+                    "line based on the analysis of its genome."
+                ),
+                "keywords": [
+                    "ancestry",
+                    "ethnic",
+                    "genetic background",
+                    "genome",
+                    "donor",
+                ],
+            },
+            "hla": {
+                "short_name": "-",
+                "description": (
+                    "HLA typing information. Alleles identified on the MHC "
+                    "type I and type II genes of the donor of a human cell "
+                    "line."
+                ),
+                "keywords": [
+                    "hla",
+                    "mhc",
+                    "typing",
+                    "alleles",
+                    "genes",
+                    "donor",
+                ],
+            },
+            "reg": {
+                "short_name": "registration",
+                "description": (
+                    "Official list, or register in which the cell line is "
+                    "registered."
+                ),
+                "keywords": [
+                    "registration",
+                    "registered",
+                    "official",
+                    "register",
+                ],
+            },
+            "var": {
+                "short_name": "sequence-variation",
+                "description": (
+                    "Important sequence variations of the cell line compared "
+                    "to the reference genome of the species."
+                ),
+                "keywords": [
+                    "variation",
+                    "mutation",
+                    "sequence",
+                    "variant",
+                    "snv",
+                    "indel",
+                ],
+            },
+            "anec": {
+                "short_name": "anecdotal",
+                "description": (
+                    "Anecdotal details regarding the cell line (its origin, "
+                    "its name or any other particularity)."
+                ),
+                "keywords": [
+                    "anecdotal",
+                    "story",
+                    "history",
+                    "background",
+                    "origin",
+                ],
+            },
+            "biot": {
+                "short_name": "biotechnology",
+                "description": (
+                    "Type of use of the cell line in a biotechnological " "context."
+                ),
+                "keywords": [
+                    "biotechnology",
+                    "biotech",
+                    "production",
+                    "manufacturing",
+                    "use",
+                ],
+            },
+            "breed": {
+                "short_name": "-",
+                "description": (
+                    "Breed or subspecies an animal cell line is derived from "
+                    "with breed identifiers from FlyBase_Strain, RS and VBO."
+                ),
+                "keywords": [
+                    "breed",
+                    "subspecies",
+                    "animal",
+                    "flybase",
+                    "strain",
+                ],
+            },
+            "caution": {
+                "short_name": "-",
+                "description": (
+                    "Errors, inconsistencies, ambiguities regarding the "
+                    "origin or other aspects of the cell line."
+                ),
+                "keywords": [
+                    "caution",
+                    "warning",
+                    "error",
+                    "inconsistency",
+                    "ambiguity",
+                ],
+            },
+            "cell": {
+                "short_name": "cell-type",
+                "description": ("Cell type from which the cell line is derived."),
+                "keywords": ["cell type", "cell", "derived", "type"],
+            },
+            "char": {
+                "short_name": "characteristics",
+                "description": (
+                    "Production process or specific biological properties of "
+                    "the cell line."
+                ),
+                "keywords": [
+                    "characteristics",
+                    "properties",
+                    "biological",
+                    "production",
+                    "process",
+                    "cancer",
+                    "tumor",
+                    "malignant",
+                ],
+            },
+            "donor": {
+                "short_name": "donor-info",
+                "description": (
+                    "Miscellaneous information relevant to the donor of the "
+                    "cell line."
+                ),
+                "keywords": [
+                    "donor",
+                    "patient",
+                    "miscellaneous",
+                    "information",
+                ],
+            },
+            "site": {
+                "short_name": "derived-from-site",
+                "description": (
+                    "Body part (tissue or organ) the cell line is derived " "from."
+                ),
+                "keywords": [
+                    "site",
+                    "tissue",
+                    "organ",
+                    "body part",
+                    "derived",
+                    "lung",
+                    "breast",
+                    "colon",
+                    "skin",
+                    "blood",
+                    "bone",
+                    "brain",
+                ],
+            },
+            "disc": {
+                "short_name": "discontinued",
+                "description": (
+                    "Discontinuation status of the cell line in a cell line " "catalog."
+                ),
+                "keywords": [
+                    "discontinued",
+                    "unavailable",
+                    "no longer available",
+                    "status",
+                ],
+            },
+            "time": {
+                "short_name": "doubling-time",
+                "description": "Population doubling-time of the cell line.",
+                "keywords": [
+                    "doubling time",
+                    "doubling",
+                    "population",
+                    "time",
+                    "hours",
+                ],
+            },
+            "from": {
+                "short_name": "-",
+                "description": (
+                    "Laboratory, research institute, university having "
+                    "established the cell line."
+                ),
+                "keywords": [
+                    "laboratory",
+                    "lab",
+                    "institute",
+                    "university",
+                    "established",
+                ],
+            },
+            "group": {
+                "short_name": "-",
+                "description": (
+                    "Specific group the cell line belongs to (example: fish "
+                    "cell lines, vaccine production cell lines)."
+                ),
+                "keywords": [
+                    "group",
+                    "fish cell lines",
+                    "vaccine production",
+                    "stem cell",
+                    "embryonic",
+                ],
+            },
+            "kar": {
+                "short_name": "karyotype",
+                "description": (
+                    "Information relevant to the chromosomes of a cell line "
+                    "(often to describe chromosomal abnormalities)."
+                ),
+                "keywords": [
+                    "karyotype",
+                    "chromosome",
+                    "chromosomal",
+                    "abnormalities",
+                    "defects",
+                ],
+            },
+            "ko": {
+                "short_name": "knockout",
+                "description": (
+                    "Gene(s) knocked-out in the cell line and method to "
+                    "obtain the KO."
+                ),
+                "keywords": ["knockout", "ko", "gene", "knocked-out"],
+            },
+            "msi": {
+                "short_name": "-",
+                "description": "Microsatellite instability degree.",
+                "keywords": ["msi", "microsatellite instability"],
+            },
+            "misc": {
+                "short_name": "miscellaneous",
+                "description": "Miscellaneous remarks about the cell line.",
+                "keywords": [
+                    "miscellaneous",
+                    "other",
+                    "additional",
+                    "notes",
+                    "remarks",
+                ],
+            },
+            "miss": {
+                "short_name": "misspelling",
+                "description": (
+                    "Identified misspelling(s) of the cell line name with in "
+                    "some case the specific publication or external resource "
+                    "entry where it appears."
+                ),
+                "keywords": ["misspelling", "misspelled", "typo"],
+            },
+            "mabi": {
+                "short_name": "mab-isotype",
+                "description": (
+                    "Monoclonal antibody isotype. Examples: IgG2a, kappa; "
+                    "IgM, lambda."
+                ),
+                "keywords": [
+                    "isotype",
+                    "igg",
+                    "igm",
+                    "iga",
+                    "ige",
+                    "monoclonal antibody",
+                ],
+            },
+            "mabt": {
+                "short_name": "mab-target",
+                "description": (
+                    "Monoclonal antibody target molecule. Generally a "
+                    "specific protein or chemical compound."
+                ),
+                "keywords": [
+                    "antibody",
+                    "mab",
+                    "target",
+                    "targeting",
+                    "protein",
+                    "molecule",
+                ],
+            },
+            "omics": {
+                "short_name": "-",
+                "description": ('"Omics" study(ies) carried out on the cell line.'),
+                "keywords": [
+                    "omics",
+                    "genomics",
+                    "transcriptomics",
+                    "proteomics",
+                    "metabolomics",
+                    "study",
+                ],
+            },
+            "part": {
+                "short_name": "part-of",
+                "description": (
+                    "The cell line belongs to a specific panel or collection "
+                    "of cell lines."
+                ),
+                "keywords": ["part", "panel", "collection", "belongs to"],
+            },
+            "pop": {
+                "short_name": "population",
+                "description": (
+                    "Ethnic group, nationality of the individual from which "
+                    "the cell line was sampled."
+                ),
+                "keywords": [
+                    "population",
+                    "ethnic",
+                    "nationality",
+                    "caucasian",
+                    "african",
+                    "asian",
+                ],
+            },
+            "prob": {
+                "short_name": "problematic",
+                "description": (
+                    "Known problem(s) related to the cell line: contaminated, "
+                    "misidentified, misclassified cell line or appearing in a "
+                    "retracted paper."
+                ),
+                "keywords": [
+                    "problematic",
+                    "contaminated",
+                    "misidentified",
+                    "problem",
+                    "retracted",
+                ],
+            },
+            "res": {
+                "short_name": "resistance",
+                "description": (
+                    "Selected to be resistant to some chemical compound "
+                    "(like a drug used in chemotherapy) or toxin. with a "
+                    "cross-reference to either ChEBI, DrugBank, NCIt or "
+                    "UniProtKB."
+                ),
+                "keywords": [
+                    "resistance",
+                    "resistant",
+                    "drug",
+                    "chemotherapy",
+                    "toxin",
+                    "cisplatin",
+                    "doxorubicin",
+                ],
+            },
+            "sen": {
+                "short_name": "senescence",
+                "description": "When a finite cell line will senesce.",
+                "keywords": ["senescence", "senescent", "finite"],
+            },
+            "int": {
+                "short_name": "integrated",
+                "description": (
+                    "Genetic element(s) integrated in the cell line: gene "
+                    "name and identifier in CGNC, FlyBase, FPbase, HGNC, MGI, "
+                    "RGD, UniProtKB, and VGNC."
+                ),
+                "keywords": ["integrated", "genetic element", "gene"],
+            },
+            "tfor": {
+                "short_name": "transformant",
+                "description": (
+                    "What caused the cell line to be transformed: generally a "
+                    "virus (with a cross-reference to NCBI taxon identifier), "
+                    "a chemical compound (with a cross-reference to ChEBI) or "
+                    "a form of irradiation (with a cross-reference to NCIt)."
+                ),
+                "keywords": [
+                    "transformant",
+                    "transformation",
+                    "virus",
+                    "chemical",
+                    "irradiation",
+                ],
+            },
+            "vir": {
+                "short_name": "virology",
+                "description": (
+                    "Susceptibility of the cell line to viral infection, "
+                    "presence of integrated viruses or any other "
+                    "virology-related information."
+                ),
+                "keywords": [
+                    "virology",
+                    "viral",
+                    "virus",
+                    "susceptibility",
+                    "infection",
+                ],
+            },
+            "cc": {
+                "short_name": "-",
+                "description": (
+                    "Comment(s). Any content described in fields "
+                    "genome-ancestry, hla, registration, sequence-variation, "
+                    "anecdotal, biotechnology, breed, caution, "
+                    "characteristics, discontinued, donor-info, "
+                    "doubling-time, from, group, karyotype, knockout, "
+                    "miscellaneous, misspelling, mab-isotype, mab-target, "
+                    "msi, omics, population, problematic, resistance, "
+                    "senescence, transfected, transformant, virology."
+                ),
+                "keywords": ["comment", "note", "remark", "observation"],
+            },
+            "str": {
+                "short_name": "-",
+                "description": "Short tandem repeat profile.",
+                "keywords": [
+                    "str",
+                    "short tandem repeat",
+                    "microsatellite",
+                    "profile",
+                ],
+            },
+            "di": {
+                "short_name": "-",
+                "description": (
+                    "Disease(s) suffered by the individual from which the "
+                    "cell line originated with its NCI Thesaurus or ORDO "
+                    "identifier."
+                ),
+                "keywords": [
+                    "disease",
+                    "condition",
+                    "leukemia",
+                    "lymphoma",
+                    "carcinoma",
+                    "sarcoma",
+                ],
+            },
+            "din": {
+                "short_name": "-",
+                "description": (
+                    "Disease(s) suffered by the individual from which the "
+                    "cell line originated, restricted to diseases having a "
+                    "NCI Thesaurus identifier."
+                ),
+                "keywords": ["disease", "nci", "thesaurus"],
+            },
+            "dio": {
+                "short_name": "-",
+                "description": (
+                    "Disease(s) suffered by the individual from which the "
+                    "cell line originated, restricted to diseases having an "
+                    "ORDO identifier."
+                ),
+                "keywords": ["disease", "ordo"],
+            },
+            "ox": {
+                "short_name": "-",
+                "description": (
+                    "Species of the individual from which the cell line "
+                    "originates with its NCBI taxon identifier."
+                ),
+                "keywords": [
+                    "species",
+                    "organism",
+                    "human",
+                    "mouse",
+                    "rat",
+                    "ncbi",
+                    "taxon",
+                ],
+            },
+            "sx": {
+                "short_name": "-",
+                "description": (
+                    "Sex of the individual from which the cell line " "originates."
+                ),
+                "keywords": [
+                    "sex",
+                    "gender",
+                    "male",
+                    "female",
+                    "man",
+                    "woman",
+                ],
+            },
+            "ag": {
+                "short_name": "-",
+                "description": (
+                    "Age at sampling time of the individual from which the "
+                    "cell line was established."
+                ),
+                "keywords": [
+                    "age",
+                    "aged",
+                    "years",
+                    "months",
+                    "days",
+                    "sampling",
+                ],
+            },
+            "oi": {
+                "short_name": "-",
+                "description": (
+                    "Cell line(s) originating from same individual (sister "
+                    "cell lines)."
+                ),
+                "keywords": [
+                    "sister",
+                    "sibling",
+                    "related",
+                    "same individual",
+                ],
+            },
+            "hi": {
+                "short_name": "-",
+                "description": (
+                    "Parent cell line from which the cell line originates."
+                ),
+                "keywords": ["parent", "derived from"],
+            },
+            "ch": {
+                "short_name": "-",
+                "description": (
+                    "Cell line(s) originated from the cell line (child cell " "lines)."
+                ),
+                "keywords": ["child", "derived", "subclone"],
+            },
+            "ca": {
+                "short_name": "-",
+                "description": (
+                    "Category to which a cell line belongs, one of 14 defined "
+                    "terms. Example: cancer cell line, hybridoma, transformed "
+                    "cell line."
+                ),
+                "keywords": [
+                    "category",
+                    "cancer cell line",
+                    "hybridoma",
+                    "transformed",
+                    "primary",
+                    "immortalized",
+                ],
+            },
+            "dt": {
+                "short_name": "-",
+                "description": (
+                    "Creation date, last modification date and version number "
+                    "of the cell line Cellosaurus entry."
+                ),
+                "keywords": ["date", "creation", "modification", "version"],
+            },
+            "dtc": {
+                "short_name": "-",
+                "description": ("Creation date of the cell line Cellosaurus entry."),
+                "keywords": [
+                    "created",
+                    "creation",
+                    "established",
+                    "founded",
+                ],
+            },
+            "dtu": {
+                "short_name": "-",
+                "description": (
+                    "Last modification date of the cell line Cellosaurus " "entry."
+                ),
+                "keywords": [
+                    "modified",
+                    "modification",
+                    "updated",
+                    "changed",
+                ],
+            },
+            "dtv": {
+                "short_name": "-",
+                "description": ("Version number of the cell line Cellosaurus entry."),
+                "keywords": ["version", "v"],
+            },
+        }
+
+        # Special species mappings with NCBI taxon IDs
+        self.species_mappings = {
+            "human": "ox:9606",
+            "homo sapiens": "ox:9606",
+            "mouse": "ox:10090",
+            "mus musculus": "ox:10090",
+            "rat": "ox:10116",
+            "rattus norvegicus": "ox:10116",
+        }
+
+        # Boolean operator patterns
+        self.boolean_patterns = [
+            (r"\b(and|&)\b", " AND "),
+            (r"\b(or|\|)\b", " OR "),
+            (r"\b(not|!)\b", " NOT "),
+        ]
+
+        # Wildcard patterns
+        self.wildcard_patterns = [
+            (r"\*", "*"),
+            (r"\?", "?"),
+        ]
+
+        # Range query patterns
+        self.range_patterns = [
+            (
+                r"\b(\d+)\s*(?:to|-)\s*(\d+)\s*(hours?|days?|years?)\b",
+                r"[\1 TO \2] \3",
+            ),
+            (
+                r"\bbetween\s+(\d+)\s+and\s+(\d+)\s*(hours?|days?|years?)\b",
+                r"[\1 TO \2] \3",
+            ),
+        ]
+
+    def run(self, arguments):
+        query = arguments.get("query")
+        include_explanation = arguments.get("include_explanation", True)
+
+        if not query:
+            return {"error": "`query` parameter is required."}
+
+        return self._convert_query(query, include_explanation)
+
+    def _calculate_similarity(self, term: str, text: str) -> float:
+        """
+        Calculate similarity between a term and text using SequenceMatcher.
+        """
+        return SequenceMatcher(None, term.lower(), text.lower()).ratio()
+
+    def _map_term_to_field(self, term: str) -> List[Tuple[str, float, str]]:
+        """
+        Map a natural language term to Cellosaurus fields based on semantic
+        similarity.
+        """
+        matches = []
+        term_lower = term.lower()
+
+        # Direct field tag matches
+        if term_lower in self.cellosaurus_fields:
+            matches.append((term_lower, 1.0, "direct_field_tag"))
+
+        # Species mappings
+        if term_lower in self.species_mappings:
+            field_tag = self.species_mappings[term_lower].split(":")[0]
+            matches.append((field_tag, 1.0, "species_mapping"))
+
+        # Keyword matching
+        for field_tag, field_info in self.cellosaurus_fields.items():
+            # Check keywords
+            for keyword in field_info["keywords"]:
+                if keyword.lower() in term_lower or term_lower in keyword.lower():
+                    similarity = self._calculate_similarity(term, keyword)
+                    matches.append((field_tag, similarity, "keyword_match:" + keyword))
+
+            # Check description similarity
+            desc_similarity = self._calculate_similarity(
+                term, field_info["description"]
+            )
+            if desc_similarity > 0.3:  # Threshold for description matching
+                matches.append((field_tag, desc_similarity, "description_match"))
+
+            # Check short name similarity
+            if field_info["short_name"] != "-":
+                short_similarity = self._calculate_similarity(
+                    term, field_info["short_name"]
+                )
+                if short_similarity > 0.3:
+                    matches.append(
+                        (
+                            field_tag,
+                            short_similarity,
+                            "short_name_match:" + field_info["short_name"],
+                        )
+                    )
+
+        # Sort by similarity score (highest first)
+        matches.sort(key=lambda x: x[1], reverse=True)
+        return matches
+
+    def _extract_field_terms(self, query: str) -> List[Tuple[str, str, float, str]]:
+        """
+        Extract field-specific terms from the query using semantic mapping.
+        """
+        terms = []
+        query_lower = query.lower()
+
+        # Split query into words and phrases
+        words = re.findall(r"\b\w+\b", query_lower)
+
+        # Also extract common phrases
+        phrases = []
+        for i in range(len(words) - 1):
+            phrases.append(f"{words[i]} {words[i+1]}")
+
+        all_terms = words + phrases
+
+        # Map each term to fields
+        for term in all_terms:
+            if len(term) < 2:  # Skip very short terms
+                continue
+
+            field_matches = self._map_term_to_field(term)
+
+            # Take the best match if confidence is high enough
+            if field_matches and field_matches[0][1] > 0.4:
+                field_tag, confidence, reason = field_matches[0]
+
+                # Handle special cases
+                if field_tag == "ox" and term in self.species_mappings:
+                    # Use the full species mapping (e.g., "ox:9606")
+                    field_tag = self.species_mappings[term]
+                    value = ""
+                else:
+                    value = term
+
+                terms.append((field_tag, value, confidence, reason))
+
+        # Remove duplicates while preserving order
+        seen = set()
+        unique_terms = []
+        for field_tag, value, confidence, reason in terms:
+            key = (field_tag, value.lower())
+            if key not in seen:
+                seen.add(key)
+                unique_terms.append((field_tag, value, confidence, reason))
+
+        return unique_terms
+
+    def _apply_boolean_operators(self, query: str) -> str:
+        """Convert natural language boolean operators to Solr syntax."""
+        result = query
+        for pattern, replacement in self.boolean_patterns:
+            result = re.sub(pattern, replacement, result, flags=re.IGNORECASE)
+        return result
+
+    def _apply_range_queries(self, query: str) -> str:
+        """Convert natural language ranges to Solr range syntax."""
+        result = query
+        for pattern, replacement in self.range_patterns:
+            result = re.sub(pattern, replacement, result, flags=re.IGNORECASE)
+        return result
+
+    def _apply_wildcards(self, query: str) -> str:
+        """Convert natural language wildcard patterns to Solr syntax."""
+        result = query
+        for pattern, replacement in self.wildcard_patterns:
+            result = re.sub(pattern, replacement, result, flags=re.IGNORECASE)
+        return result
+
+    def _construct_solr_query(
+        self, terms: List[Tuple[str, str, float, str]], original_query: str
+    ) -> str:
+        """Construct the final Solr query from extracted terms."""
+        if not terms:
+            # If no field-specific terms found, return original query as
+            # general search
+            return self._apply_boolean_operators(original_query.strip())
+
+        # Build field-specific queries
+        field_queries = []
+        for field_tag, value, _confidence, _reason in terms:
+            # Handle special field mappings that already include values
+            # (like ox:9606)
+            if ":" in field_tag and not value:
+                field_queries.append(field_tag)
+            elif ":" in field_tag and value:
+                # Handle cases like "ox:9606" with additional value
+                field_queries.append(
+                    f"{field_tag} AND {field_tag.split(':')[0]}:{value}"
+                )
+            else:
+                # Escape special characters in values
+                escaped_value = re.sub(r'([+\-&|!(){}[\]^"~*?:\\/])', r"\\\1", value)
+                field_queries.append(f"{field_tag}:{escaped_value}")
+
+        # Join with AND by default (most restrictive)
+        if len(field_queries) == 1:
+            return field_queries[0]
+        else:
+            return f"({' AND '.join(field_queries)})"
+
+    def _validate_solr_query(self, query: str) -> Tuple[bool, str]:
+        """Basic validation of Solr query syntax."""
+        try:
+            # Check for balanced parentheses
+            paren_count = query.count("(") - query.count(")")
+            if paren_count != 0:
+                return False, f"Unbalanced parentheses in query: {query}"
+
+            # Check for balanced brackets in ranges
+            bracket_count = query.count("[") - query.count("]")
+            if bracket_count != 0:
+                return False, f"Unbalanced brackets in range query: {query}"
+
+            # Check for empty field queries
+            if re.search(r":\s*$", query):
+                return False, f"Empty field value in query: {query}"
+
+            return True, "Valid Solr query"
+
+        except Exception as e:
+            return False, f"Query validation error: {str(e)}"
+
+    def _convert_query(
+        self, natural_query: str, include_explanation: bool = True
+    ) -> Dict[str, Any]:
+        """
+        Convert natural language query to Solr syntax using systematic field
+        mapping.
+        """
+        try:
+            # Normalize input
+            normalized_query = natural_query.lower()
+            # Replace common conjunctions with spaces for better term
+            # extraction
+            normalized_query = re.sub(
+                r"\b(with|from|in|of|for)\b", " ", normalized_query
+            )
+            # Remove extra whitespace
+            normalized_query = re.sub(r"\s+", " ", normalized_query)
+
+            # Apply transformations
+            processed_query = self._apply_boolean_operators(normalized_query)
+            processed_query = self._apply_range_queries(processed_query)
+            processed_query = self._apply_wildcards(processed_query)
+
+            # Extract field-specific terms using semantic mapping
+            terms = self._extract_field_terms(natural_query)
+
+            # Construct Solr query
+            solr_query = self._construct_solr_query(terms, processed_query)
+
+            # Validate the query
+            is_valid, validation_msg = self._validate_solr_query(solr_query)
+
+            result = {
+                "success": True,
+                "original_query": natural_query,
+                "solr_query": solr_query,
+                "is_valid": is_valid,
+                "validation_message": validation_msg,
+            }
+
+            if include_explanation:
+                result["explanation"] = {
+                    "extracted_terms": [
+                        {
+                            "field": field_tag,
+                            "value": value,
+                            "confidence": confidence,
+                            "match_reason": reason,
+                        }
+                        for field_tag, value, confidence, reason in terms
+                    ],
+                    "transformations_applied": [
+                        "boolean_operators",
+                        "range_queries",
+                        "wildcards",
+                    ],
+                    "available_fields": list(self.cellosaurus_fields.keys()),
+                }
+
+            return result
+
+        except Exception as e:
+            return {
+                "success": False,
+                "error": f"Query conversion failed: {e}",
+                "original_query": natural_query,
+            }
+
+
+@register_tool("CellosaurusGetCellLineInfoTool")
+class CellosaurusGetCellLineInfoTool(BaseTool):
+    """
+    Tool to get detailed information about a specific cell line using its
+    accession number.
+    """
+
+    def __init__(self, tool_config, base_url="https://api.cellosaurus.org"):
+        super().__init__(tool_config)
+        self.base_url = base_url
+        self.timeout_seconds = int(os.environ.get("CELLOSAURUS_TIMEOUT", "30"))
+
+    def run(self, arguments):
+        accession = arguments.get("accession")
+        format_type = arguments.get("format", "json")
+        fields = arguments.get("fields")
+
+        if not accession:
+            return {"error": "`accession` parameter is required."}
+
+        return self._get_cell_line_info(accession, format_type, fields)
+
+    def _get_cell_line_info(self, accession, format_type, fields):
+        """Get detailed cell line information by accession number."""
+        try:
+            # Validate accession format
+            # (Cellosaurus accessions start with CVCL_)
+            if not accession.startswith("CVCL_"):
+                return {
+                    "error": (
+                        "Accession must start with 'CVCL_' " "(Cellosaurus format)"
+                    )
+                }
+
+            # Validate format
+            valid_formats = ["json", "xml", "txt", "fasta"]
+            if format_type not in valid_formats:
+                return {
+                    "error": ("Format must be one of: " f"{', '.join(valid_formats)}")
+                }
+
+            # Validate fields if provided
+            if fields is not None:
+                if not isinstance(fields, list):
+                    return {"error": "Fields must be a list of field names"}
+
+                # Valid Cellosaurus field tags
+                valid_fields = {
+                    "id",
+                    "sy",
+                    "idsy",
+                    "ac",
+                    "acas",
+                    "dr",
+                    "ref",
+                    "rx",
+                    "ra",
+                    "rt",
+                    "rl",
+                    "ww",
+                    "anc",
+                    "hla",
+                    "reg",
+                    "var",
+                    "anec",
+                    "biot",
+                    "breed",
+                    "caution",
+                    "cell",
+                    "char",
+                    "donor",
+                    "site",
+                    "disc",
+                    "time",
+                    "from",
+                    "group",
+                    "kar",
+                    "ko",
+                    "msi",
+                    "misc",
+                    "miss",
+                    "mabi",
+                    "mabt",
+                    "omics",
+                    "part",
+                    "pop",
+                    "prob",
+                    "res",
+                    "sen",
+                    "int",
+                    "tfor",
+                    "vir",
+                    "cc",
+                    "str",
+                    "di",
+                    "din",
+                    "dio",
+                    "ox",
+                    "sx",
+                    "ag",
+                    "oi",
+                    "hi",
+                    "ch",
+                    "ca",
+                    "dt",
+                    "dtc",
+                    "dtu",
+                    "dtv",
+                }
+
+                invalid_fields = set(fields) - valid_fields
+                if invalid_fields:
+                    return {"error": f"Invalid fields: {list(invalid_fields)}"}
+
+            # Prepare request parameters
+            params = {"format": format_type}
+            if fields:
+                params["fields"] = ",".join(fields)
+
+            # Make API request
+            url = f"{self.base_url}/cell-line/{accession}"
+            headers = {"Accept": f"application/{format_type}"}
+
+            resp = requests.get(
+                url,
+                params=params,
+                headers=headers,
+                timeout=self.timeout_seconds,
+            )
+            resp.raise_for_status()
+
+            # Parse response based on format
+            if format_type == "json":
+                data = resp.json()
+
+                # Extract cell line data from nested structure
+                cell_line_data = None
+                if isinstance(data, dict) and "Cellosaurus" in data:
+                    cellosaurus_data = data["Cellosaurus"]
+                    if (
+                        "cell-line-list" in cellosaurus_data
+                        and cellosaurus_data["cell-line-list"]
+                    ):
+                        cell_line_data = cellosaurus_data["cell-line-list"][0]
+
+                if not cell_line_data:
+                    return {
+                        "error": (
+                            "No cell line data found for accession " f"{accession}"
+                        )
+                    }
+
+                # Apply field filtering if requested
+                if fields:
+                    filtered_data = {}
+                    for field in fields:
+                        if field in cell_line_data:
+                            filtered_data[field] = cell_line_data[field]
+                    cell_line_data = filtered_data
+
+                return {
+                    "success": True,
+                    "accession": accession,
+                    "data": cell_line_data,
+                    "format": format_type,
+                }
+            else:
+                # For non-JSON formats, return the raw content
+                return {
+                    "success": True,
+                    "accession": accession,
+                    "data": resp.text,
+                    "format": format_type,
+                }
+
+        except requests.HTTPError as http_err:
+            status = getattr(http_err.response, "status_code", None)
+            if status == 404:
+                return {"error": f"Cell line with accession {accession} not found"}
+            return {"error": f"HTTP {status}: {http_err}"}
+        except Exception as e:
+            return {"error": str(e)}