Search.setIndex({"docnames": ["bionty.BFXPipeline", "bionty.Bionty", "bionty.CellLine", "bionty.CellMarker", "bionty.CellType", "bionty.Disease", "bionty.Drug", "bionty.Gene", "bionty.LOCAL_SOURCES", "bionty.Ontology", "bionty.Pathway", "bionty.Phenotype", "bionty.Protein", "bionty.Readout", "bionty.Species", "bionty.Tissue", "bionty.dev", "bionty.dev.ontology_info", "bionty.display_available_sources", "bionty.display_currently_used_sources", "bionty.reset_sources", "changelog", "guide/concepts", "guide/config", "guide/extend", "guide/index", "guide/inspect", "guide/lookup", "guide/ontology", "index", "reference"], "filenames": ["bionty.BFXPipeline.rst", "bionty.Bionty.rst", "bionty.CellLine.rst", "bionty.CellMarker.rst", "bionty.CellType.rst", "bionty.Disease.rst", "bionty.Drug.rst", "bionty.Gene.rst", "bionty.LOCAL_SOURCES.rst", "bionty.Ontology.rst", "bionty.Pathway.rst", "bionty.Phenotype.rst", "bionty.Protein.rst", "bionty.Readout.rst", "bionty.Species.rst", "bionty.Tissue.rst", "bionty.dev.rst", "bionty.dev.ontology_info.rst", "bionty.display_available_sources.rst", "bionty.display_currently_used_sources.rst", "bionty.reset_sources.rst", "changelog.md", "guide/concepts.md", "guide/config.md", "guide/extend.md", "guide/index.md", "guide/inspect.ipynb", "guide/lookup.ipynb", "guide/ontology.ipynb", "index.md", "reference.md"], "titles": ["bionty.BFXPipeline", "bionty.Bionty", "bionty.CellLine", "bionty.CellMarker", "bionty.CellType", "bionty.Disease", "bionty.Drug", "bionty.Gene", "bionty.LOCAL_SOURCES", "bionty.Ontology", "bionty.Pathway", "bionty.Phenotype", "bionty.Protein", "bionty.Readout", "bionty.Species", "bionty.Tissue", "bionty.dev", "bionty.dev.ontology_info", "bionty.display_available_sources", "bionty.display_currently_used_sources", "bionty.reset_sources", "Changelog", "Concepts", "Configuration", "Extend Bionty", "Bionty: Basic biological entities", "Inspect &amp; map identifiers", "Look up records of species, gene, protein, cell marker", "Access ontologies: cell type, tissue, disease, phenotype", "Bionty", "Reference"], "terms": {"class": [0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 27, 28, 30], "speci": [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 15, 19, 21, 22, 23, 24, 25, 26, 28], "all": [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 18, 19, 23, 24, 25, 26, 27, 28], "sourc": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 26, 27, 28, 30], "none": [0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28], "version": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 19, 21, 22, 24, 25, 26, 27, 28], "kwarg": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 24], "base": [0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 21, 22, 25, 30], "bioinformat": [0, 28], "pipelin": [0, 28], "paramet": [0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 21, 24, 27], "name": [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 27, 28], "entiti": [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 19, 21, 23, 24, 26, 27, 28, 30], "The": [0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 26, 27, 28], "kei": [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 21], "local": [0, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 20, 21, 24, 25, 27], "yml": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 21, 24], "file": [0, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 20, 21, 24, 25, 26, 28], "get": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 17], "avail": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 18, 21, 23, 24, 25, 26, 27, 28], "databas": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 21, 26, 28], "display_available_sourc": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 23, 25, 28], "ontologi": [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 17, 21, 22, 26, 27], "typic": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 22], "date": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 21], "an": [0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 26, 27, 28], "actual": [0, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 21], "attribut": [0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15], "properti": [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 21, 22, 24], "method": [0, 1, 3, 7, 9, 12, 13, 14, 21], "df": [0, 1, 3, 7, 12, 13, 14, 21, 25, 26, 27, 28], "datafram": [0, 1, 3, 7, 12, 13, 14, 18, 19, 26, 27], "return": [0, 1, 3, 7, 8, 12, 13, 14, 17, 18, 19, 21, 26], "type": [0, 1, 3, 4, 7, 12, 13, 14, 17, 18, 19, 21, 22, 24, 25, 26, 27], "include_id_prefix": 1, "object": [1, 7, 8, 22, 26, 27, 28], "biolog": [1, 22, 28], "see": [1, 3, 7, 9, 12, 13, 14, 24, 25, 27], "basic": 1, "background": 1, "panda": [1, 13, 26, 27], "A": [1, 7, 21, 26, 28], "exampl": [1, 7, 18, 19, 22, 23, 24, 26, 27, 28], "import": [1, 7, 9, 18, 19, 21, 24, 25, 26, 27, 28, 30], "bt": [1, 7, 18, 19, 25, 27, 28, 30], "gene": [1, 10, 21, 22, 25, 28], "fuzzy_match": [1, 21, 25, 26], "string": [1, 21, 25], "field": [1, 7, 21, 26, 27], "synonyms_field": [1, 26], "synonym": [1, 21, 25, 27, 28], "case_sensit": [1, 21], "true": [1, 24, 26], "return_ranked_result": [1, 26], "fals": [1, 20, 26], "fuzzi": [1, 25], "match": [1, 21, 25], "given": [1, 22], "against": [1, 21, 26], "input": [1, 21], "valu": [1, 7, 22, 26], "biontyfield": [1, 21], "i": [1, 7, 9, 12, 19, 21, 22, 23, 24, 25, 26, 27, 28], "also": [1, 9, 13, 21, 23, 26, 27], "map": [1, 21, 22], "If": [1, 24], "whether": [1, 26], "case": [1, 21, 24], "sensit": [1, 21], "entri": [1, 21, 23, 27], "rank": [1, 26], "ratio": [1, 26], "str": [1, 24], "best": 1, "celltype_bionti": [1, 25], "celltyp": [1, 21, 23, 25, 28], "gamma": [1, 25], "delta": [1, 25], "t": [1, 23, 24, 25, 26, 27, 28], "cell": [1, 2, 3, 4, 21, 22, 24, 25, 26], "inspect": [1, 21], "identifi": [1, 27], "return_df": [1, 26], "list": [1, 23, 26], "ar": [1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 28], "mappabl": [1, 25, 26], "refer": [1, 21, 22, 26], "check": [1, 21, 25, 26], "compar": 1, "ontology_id": [1, 21, 26, 28], "id": [1, 9, 21, 22, 26, 27], "union": 1, "dict": [1, 17], "dictionari": 1, "specifi": [1, 23, 25, 27], "curat": [1, 21, 23, 26], "index": [1, 7, 12, 14, 21, 26, 27, 28], "boolean": [1, 26], "__mapped__": [1, 26], "column": [1, 21, 22, 26], "indic": [1, 26], "complianc": 1, "default": [1, 7, 12, 21, 24, 26, 27], "boettcher": 1, "bone": 1, "marrow": 1, "ct": 1, "lookup": [1, 7, 21, 25, 26, 28], "auto": [1, 7, 26, 27], "complet": [1, 7, 26, 27, 28], "tupl": [1, 7], "namedtupl": [1, 7, 21], "inform": [1, 7, 17, 27], "gene_bionty_lookup": [1, 25, 27], "tef": [1, 7], "map_synonym": [1, 21, 25, 26], "return_mapp": [1, 26], "repres": 1, "gene_bionti": [1, 25, 26, 27], "ensembl": [1, 7, 14, 21, 25, 27, 28], "releas": [1, 23, 24, 27, 28], "108": [1, 21, 27, 28], "gene_symbol": [1, 21, 26, 27], "a1cf": [1, 26], "a1bg": [1, 25, 26], "fancd1": [1, 25, 26, 27], "fancd20": 1, "gn": 1, "symbol": [1, 7, 21, 25, 26, 27], "line": [2, 24, 25, 28], "1": [2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 21, 26, 27, 28], "edit": [2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 23], "term": [2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 22, 26, 27], "coordin": [2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15], "review": [2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15], "clo": [2, 28], "human": [3, 5, 7, 11, 12, 21, 23, 24, 25, 26, 27, 28], "marker": [3, 21, 26], "http": [3, 6, 7, 9, 10, 11, 12, 13, 14, 23, 24, 28], "bio": [3, 28], "bigdata": [3, 28], "hrbmu": [3, 28], "edu": [3, 28], "cn": [3, 28], "ingest": [3, 7, 12, 14], "lamin": [3, 7, 8, 12, 14, 21, 23, 24, 27, 28], "ai": [3, 7, 12, 14, 28], "doc": [3, 7, 12, 14, 21, 28], "asset": [3, 7, 12, 14, 21, 23, 28], "2": [3, 5, 10, 21, 26, 27, 28], "0": [3, 21, 26, 27, 28], "obophenotyp": [4, 15, 28], "mondo": [5, 23, 24, 25, 28], "monarch": 5, "initi": [5, 21, 24, 27], "diseaseontologi": 5, "humandiseaseontologi": 5, "dron": [6, 28], "bioport": [6, 10, 28], "bioontologi": [6, 10, 28], "org": [6, 7, 10, 11, 12, 14, 23, 24, 28], "www": [7, 12, 13, 14, 28], "note": [7, 23], "biotyp": 7, "info": 7, "genom": 7, "genebuild": [7, 27], "html": [7, 9, 14, 28], "gene_nam": [7, 26, 27], "ensembl_gene_id": [7, 26, 27], "gene_lookout": 7, "posixpath": 8, "home": [8, 23, 24, 27], "runner": [8, 27], "yaml": [8, 21, 24, 25, 27], "path": [8, 9, 21, 24], "subclass": [8, 24], "non": [8, 21, 26], "window": [8, 21], "system": [8, 28], "On": 8, "posix": 8, "instanti": [8, 26], "should": [8, 26], "thi": [8, 23, 24, 26], "handl": [9, 21], "import_depth": 9, "timeout": [9, 21, 28], "100": [9, 21, 26, 28], "thread": 9, "prefix": [9, 21, 23], "interfac": 9, "via": [9, 27, 28], "pronto": [9, 21, 26, 27, 28], "readthedoc": 9, "io": [9, 28], "en": 9, "stabl": 9, "api": [9, 16, 21, 30], "maximum": [9, 23], "depth": 9, "resolv": 9, "tree": 9, "second": 9, "us": [9, 19, 21, 22, 23, 24, 25, 26, 27, 28], "when": [9, 21, 23, 24, 28], "perform": 9, "network": 9, "o": [9, 28], "number": [9, 26], "pars": [9, 21, 28], "url": [9, 21, 23, 24, 28], "dev": [9, 21, 30], "onli": [9, 21, 26, 27], "get_term": [9, 21], "search": [9, 27], "its": [9, 21, 23], "write_obo": 9, "write": [9, 21], "dynamicdir": 9, "filenam": [9, 21], "obo": [9, 23, 24, 28], "go": [10, 17, 21, 28], "p": [10, 26], "summari": [10, 21], "pw": [10, 28], "hpo": [11, 28], "jax": [11, 28], "app": 11, "uniprot": [12, 25, 27, 28], "uniprotkb_id": [12, 26, 27], "experiment": [13, 25, 28], "factor": [13, 25, 27, 28], "ebi": [13, 28], "ac": [13, 28], "uk": [13, 28], "ol": [13, 17, 21, 28], "efo": [13, 17, 28], "uberon": [15, 25, 28], "develop": [16, 21], "namespac": 17, "latest": [17, 21], "from": [17, 21, 22, 24, 26, 27, 28], "e": [17, 22, 23], "g": [17, 22, 23, 27], "cl": [17, 23, 26, 28], "displai": [18, 19, 21, 25], "current": [19, 21, 23, 24, 25, 28], "activ": [19, 21, 23], "uniqu": [19, 21], "confirm": 20, "reset": 20, "pr": 21, "user": [21, 22, 23, 24], "patch": 21, "fix": [21, 26], "bug": 21, "429": 21, "sunnyosun": 21, "2023": [21, 23, 24, 25, 28], "06": [21, 23, 24, 27, 28], "12": [21, 27], "20": [21, 27], "improv": 21, "log": [21, 26], "428": 21, "remov": 21, "updat": [21, 24], "guid": [21, 24], "break": [21, 24], "419": 21, "lamindb": 21, "instanc": 21, "error": 21, "refactor": 21, "417": 21, "11": [21, 23, 24, 26, 27, 28], "19": [21, 28], "No": 21, "longer": 21, "compat": 21, "411": 21, "10": [21, 23, 24, 26, 27, 28], "alwai": [21, 26], "regener": 21, "current_sourc": 21, "upon": 21, "410": 21, "lamindb_instance_load": 21, "409": 21, "koncopd": 21, "notebook": 21, "execut": 21, "408": 21, "falexwolf": 21, "renam": [21, 26], "variabl": [21, 22], "407": 21, "18": 21, "clean": 21, "up": [21, 28], "depend": [21, 26], "406": 21, "environ": [21, 28], "load": [21, 26], "405": 21, "09": [21, 27], "move": 21, "img": 21, "folder": 21, "404": 21, "re": 21, "organ": [21, 28], "403": 21, "08": [21, 27, 28], "ref": 21, "402": 21, "17": 21, "everywher": 21, "possibl": [21, 26], "401": 21, "07": [21, 27], "17a3": 21, "parse_current_vers": 21, "400": 21, "harmon": 21, "399": 21, "zethson": 21, "readout": [21, 25], "398": 21, "17a1": 21, "add": [21, 24], "test": 21, "gener": [21, 26, 27, 28, 30], "397": 21, "same": [21, 22, 26, 27], "code": 21, "creat": [21, 27], "396": 21, "chang": [21, 23, 27], "format": 21, "have": [21, 22, 23, 26, 28], "394": 21, "04": [21, 27, 28], "support": [21, 24], "392": 21, "nox": 21, "venv": 21, "388": 21, "01": [21, 23, 24, 25, 27, 28], "16": [21, 27, 28], "global": 21, "387": 21, "05": [21, 27, 28], "31": 21, "385": 21, "30": [21, 23, 24, 25, 28], "384": 21, "delet": 21, "incomplet": 21, "except": 21, "s3_bionty_asset": 21, "383": 21, "29": 21, "nbproject": 21, "product": [21, 28], "382": 21, "ad": [21, 22, 24], "bionti": [21, 26, 27, 28, 30], "backward": 21, "381": 21, "15": [21, 28], "implement": [21, 24], "first": [21, 23, 26], "380": 21, "decreas": 21, "refresh_per_second": 21, "progress": [21, 24], "bar": 21, "379": 21, "28": [21, 26, 27], "replac": [21, 26], "upath": 21, "fsspec": 21, "botocor": 21, "376": 21, "unus": 21, "377": 21, "allow": [21, 22, 28], "everi": [21, 22], "375": 21, "includ": [21, 28], "definit": [21, 26, 28], "parquet": 21, "372": 21, "27": [21, 28], "370": 21, "25": [21, 26], "prettifi": 21, "repr": 21, "369": 21, "download": [21, 23, 24, 28], "s3": [21, 23, 28], "365": 21, "14": [21, 28], "359": 21, "24": 21, "children": [21, 22, 26, 28], "363": 21, "23": 21, "356": 21, "do": 21, "metadata": [21, 26], "355": 21, "13": 21, "drug": [21, 25, 28], "352": 21, "process": [21, 28], "safe": 21, "350": 21, "jlricon": 21, "5": [21, 26], "lowercas": 21, "348": 21, "4": [21, 22, 26, 27], "lndb": 21, "347": 21, "3": [21, 22, 26, 27, 28], "intern": 21, "ffspec": 21, "346": 21, "lndb_storag": 21, "344": 21, "cellmark": [21, 25, 27, 28], "340": 21, "deprec": 21, "341": 21, "339": 21, "338": 21, "more": [21, 24, 28], "flexibl": 21, "337": 21, "02": [21, 23, 24, 27, 28], "print": [21, 23, 24, 28], "336": 21, "pin": 21, "storag": 21, "333": 21, "lnschema": 21, "332": 21, "_entiti": 21, "privat": 21, "326": 21, "pathwai": [21, 25, 28], "329": 21, "26": 21, "upload": 21, "325": 21, "sync": 21, "stage": 21, "main": 21, "316": [21, 27], "empti": 21, "314": 21, "6": [21, 26, 27], "make": [21, 26], "sure": 21, "na": 21, "present": 21, "313": 21, "cached_properti": 21, "dep": 21, "py3": 21, "7": [21, 26, 27, 28], "312": 21, "speed": 21, "305": 21, "ci": 21, "293": 21, "new": [21, 22, 26, 27], "290": 21, "03": [21, 27, 28], "try": [21, 26], "289": 21, "protein": [21, 25, 28], "288": 21, "287": 21, "284": 21, "lookup_col": 21, "lookup_field": [21, 27], "283": 21, "update_default": 21, "280": 21, "279": 21, "268": 21, "removeprefix": 21, "8": 21, "277": 21, "22": 21, "274": 21, "271": 21, "21": [21, 26, 28], "ensur": [21, 26], "269": 21, "9": [21, 27, 28], "267": 21, "0rc1": 21, "function": [21, 24, 28], "264": 21, "infer": 21, "db": 21, "pass": [21, 24, 26], "256": 21, "257": 21, "md5": [21, 23, 24, 28], "sum": [21, 24], "249": 21, "output": 21, "255": 21, "full": [21, 24], "record": [21, 22], "254": 21, "imag": 21, "253": 21, "link": [21, 23, 26], "252": 21, "keep": 21, "250": 21, "order": [21, 23], "248": 21, "datadir": 21, "245": 21, "244": 21, "take": [21, 22, 26, 27], "bullet": 21, "240": 21, "8rc2": 21, "build": 21, "239": 21, "document": 21, "220": 21, "234": 21, "websit": [21, 23, 24], "per": 21, "rich": 21, "tabl": [21, 22, 26], "232": 21, "better": 21, "docstr": 21, "decor": 21, "231": 21, "230": 21, "8rc1": 21, "celllin": [21, 25, 28], "229": 21, "simplifi": 21, "227": 21, "deduc": 21, "fly": 21, "entit": 21, "223": 21, "faq": 21, "218": 21, "access": [21, 23, 25, 26, 27], "217": 21, "216": 21, "entityt": 21, "214": 21, "laminci": 21, "213": 21, "hca": 21, "209": 21, "202": [21, 28], "205": 21, "206": 21, "201": 21, "hdo": 21, "multipl": 21, "187": 21, "gh": 21, "workflow": 21, "188": 21, "lndb_setup": 21, "189": 21, "bpenteado": 21, "phenotyp": [21, 25], "172": 21, "183": 21, "land": 21, "page": 21, "182": 21, "_logger": 21, "py": 21, "176": 21, "167": 21, "168": 21, "lamindoc": 21, "secret": [21, 26], "173": 21, "169": 21, "166": 21, "common_nam": 21, "165": 21, "separ": 21, "___": 21, "164": 21, "162": 21, "expand": 21, "python": [21, 25, 28], "161": 21, "pull": 21, "dynam": 21, "160": 21, "progressbar": 21, "159": 21, "157": 21, "2022": [21, 23, 24, 27, 28], "156": 21, "ontology_info": 21, "155": 21, "153": 21, "most": [21, 22, 23, 28], "recent": [21, 23], "_current": 21, "152": 21, "fetch": 21, "151": 21, "bioreadout": 21, "150": 21, "track": [21, 22], "149": 21, "148": 21, "147": 21, "146": 21, "145": 21, "cach": [21, 23], "144": 21, "143": 21, "tissu": [21, 25], "142": 21, "switch": 21, "cloudpath": 21, "141": 21, "140": 21, "139": 21, "138": 21, "137": 21, "136": 21, "135": 21, "migrat": 21, "134": 21, "feature_model": 21, "133": 21, "redefin": 21, "132": [21, 27], "todict": 21, "131": 21, "duplic": [21, 27], "130": 21, "descript": [21, 27], "128": 21, "127": 21, "tutori": 21, "125": 21, "cell_typ": [21, 28], "diseas": [21, 23, 24, 25], "123": 21, "cell_mark": [21, 26, 27], "fit": 21, "schema": 21, "122": 21, "121": 21, "120": 21, "119": 21, "118": 21, "etc": [21, 22], "117": 21, "116": 21, "115": 21, "114": 21, "113": 21, "112": 21, "n_map": 21, "111": 21, "gene_id": 21, "110": 21, "109": 21, "entrez_gene_id": 21, "int": 21, "display_nam": 21, "so": [21, 26, 27], "107": [21, 28], "increas": [21, 26], "106": 21, "modifi": [21, 24], "104": 21, "103": 21, "dure": 21, "modul": 21, "98": 21, "97": 21, "shortcut": 21, "look": [21, 28], "static": 21, "set": [21, 24, 26, 27, 28], "96": 21, "logger": 21, "95": 21, "standard": [21, 27], "93": 21, "alia": 21, "92": [21, 26], "89": 21, "88": 21, "87": 21, "prototyp": 21, "86": 21, "polish": 21, "85": [21, 26], "mgi": [21, 25, 27], "mous": [21, 27, 28], "feather": 21, "hgnc": [21, 25, 26, 27], "84": 21, "back": 21, "83": [21, 26], "hard": 21, "82": 21, "81": 21, "data": [21, 24, 26, 28, 30], "80": 21, "our": [21, 26], "bucket": 21, "79": [21, 28], "quickstart": 21, "78": [21, 26], "coverag": 21, "setup": 21, "77": 21, "collect": [21, 26], "nb": 21, "76": 21, "badg": 21, "codecov": 21, "pypi": 21, "pre": 21, "commit": 21, "75": [21, 26], "73": 21, "iter": 21, "readabl": 21, "71": [21, 26], "dataclass": 21, "67": 21, "66": 21, "pickl": 21, "65": 21, "1a3": 21, "62": 21, "1a2": 21, "rewrit": 21, "task": 21, "61": 21, "59": 21, "58": 21, "tak": 21, "56": 21, "55": 21, "1a1": 21, "54": 21, "request": 21, "async": 21, "53": 21, "warn": [21, 26], "52": 21, "dual": 21, "usag": 21, "51": 21, "taxon": 21, "50": [21, 26], "made": 21, "own": [21, 23], "45": 21, "propos": 21, "design": [21, 24, 27], "44": 21, "43": 21, "work": [21, 24, 27, 28], "ani": [21, 26, 28], "41": 21, "manag": [21, 22, 24, 25], "40": 21, "introduc": 21, "38": 21, "36": 21, "34": [21, 27], "let": [22, 26, 27], "": [22, 26, 27, 28], "defin": [22, 24, 26, 28], "vocabulari": [22, 28], "mean": 22, "There": 22, "differ": [22, 26, 27], "roughli": 22, "equival": 22, "For": [22, 23, 24, 26, 27, 28], "one": [22, 24, 26], "can": [22, 23, 24, 26, 27, 28], "describ": [22, 28], "scientif": 22, "common": [22, 23], "granular": 22, "often": 22, "hierarch": 22, "public": [22, 25], "contain": [22, 26, 27], "addit": [22, 26], "custom": [22, 23, 25], "correspond": [22, 27], "knowledg": [22, 24], "absent": 22, "state": 22, "synthet": 22, "central": [22, 28], "model": [22, 27, 30], "abov": 22, "mention": 22, "come": [22, 28], "which": [22, 24, 26, 27, 28], "each": [22, 23], "altern": 22, "ha": [22, 28], "hierarchi": 22, "amount": 22, "bioregistri": [22, 25], "we": [22, 23, 24, 26, 27, 28], "recommend": [22, 24], "sql": 22, "extens": 22, "lnschema_bionti": [22, 25], "maintain": 23, "These": [23, 24], "bioni": 23, "store": [23, 26], "provid": [23, 28], "fast": 23, "reliabl": 23, "your": [23, 25], "_dynam": [23, 28], "directori": [23, 24], "content": 23, "ident": 23, "freshli": [23, 28], "instal": 23, "mai": [23, 26, 27, 28], "display_currently_used_sourc": [23, 25, 28], "short": 23, "curi": 23, "appli": [23, 24], "To": [23, 25, 26, 27, 28], "shift": 23, "follow": [23, 24, 27, 28], "doid": [23, 24, 25, 28], "highlight": 23, "consid": 23, "purl": [23, 24, 28], "obolibrari": [23, 24, 28], "owl": [23, 24, 28], "2b7d479d4bd02a94eab47d1c9e64c5db": [23, 24, 28], "04b808d05c2c2e81430b20a0e87552bb": [23, 24, 28], "monarchin": [23, 24, 28], "9f0c92ad2896dda82195e9226a06dc36": [23, 24, 28], "inhouse_diseas": [23, 24], "2000": [23, 24], "my": [23, 24], "com": [23, 24, 28], "mydiseas": [23, 24], "leav": [23, 24], "out": [23, 24], "row": [23, 24], "hous": [23, 24, 25], "won": [23, 26], "effect": 23, "taken": 23, "variou": 24, "wai": 24, "cover": 24, "how": [24, 26, 27], "exist": [24, 28], "doe": 24, "you": [24, 26, 27, 28], "d": [24, 28], "like": 24, "enabl": [24, 26], "featur": [24, 26], "where": [24, 28], "run": [24, 26], "standalon": 24, "kindli": 24, "ask": 24, "patienc": 24, "sinc": 24, "easiest": 24, "adapt": 24, "associ": [24, 27], "doesn": 24, "unknown": 24, "option": [24, 26], "calcul": 24, "hashlib": 24, "pathlib": 24, "def": 24, "calculate_md5": 24, "file_path": 24, "open": 24, "rb": 24, "f": [24, 26], "while": 24, "read": 24, "8192": 24, "file_md5": 24, "hexdigest": 24, "desir": 24, "configur": 24, "detail": [24, 25], "requir": 24, "sever": 24, "automat": 24, "popul": 24, "either": 24, "explicitli": 24, "henc": 24, "myentiti": 24, "would": 24, "__init__": 24, "self": 24, "liter": 24, "mydatabase_1": 24, "mydatabase_2": 24, "super": 24, "need": [24, 26], "mysource_1": 24, "2042": 24, "mysource_2": 24, "great": 24, "now": [24, 26], "ve": 24, "eas": 25, "along": [25, 28], "ncbi": 25, "taxonomi": 25, "bfxpipelin": [25, 28], "larg": [25, 28], "nf": 25, "core": 25, "didn": 25, "favorit": 25, "extend": [25, 28], "packag": [25, 28, 30], "pip": 25, "lnma": 25, "onto": 25, "local_sourc": 25, "queryabl": 26, "compli": 26, "chosen": 26, "directli": [26, 28], "offer": 26, "pd": 26, "illustr": 26, "u": 26, "some": 26, "corrupt": 26, "24086": 26, "1101": [26, 27], "ensg00000148584": 26, "ensg00000121410": 26, "ensg00000188389": 26, "ensgcorrupt": 26, "df_orig": 26, "set_index": 26, "tip": 26, "not_map": 26, "procedur": 26, "convert": [26, 27], "them": [26, 27], "appar": 26, "further": 26, "mapped_symbol_synonym": 26, "brca2": [26, 27, 28], "mapper": 26, "df_curat": 26, "reset_index": 26, "wa": 26, "terminologi": 26, "might": 26, "section": 26, "demonstr": 26, "unmatch": 26, "whose": 26, "valid": 26, "invalid": 26, "antibodi": 26, "target": 26, "time": 26, "flow": 26, "cytometri": 26, "dataset": 26, "ki67": 26, "ccr7x": 26, "cd14": 26, "cd8": 26, "cd45ra": 26, "cd4": 26, "cd3": 26, "cd127": 26, "pd1": 26, "cd66b": 26, "siglec8": 26, "cell_marker_bionti": [26, 27], "autocomplet": [26, 27], "just": [26, 27], "head": [26, 27, 28], "ncbi_gene_id": [26, 27], "cm_mertk": [26, 27], "mertk": [26, 27], "10461": [26, 27], "mer": [26, 27], "proto": [26, 27], "oncogen": [26, 27], "tyrosin": [26, 27], "kinas": [26, 27], "q12866": [26, 27], "cm_cd16": [26, 27], "cd16": [26, 27], "2215": [26, 27], "fcgr3a": [26, 27], "fc": [26, 27], "fragment": [26, 27], "igg": [26, 27], "receptor": [26, 27, 28], "iiib": [26, 27], "o75015": [26, 27], "cm_cd206": [26, 27], "cd206": [26, 27], "4360": [26, 27], "mrc1": [26, 27], "mannos": [26, 27], "c": [26, 27], "p22897": [26, 27], "cm_crig": [26, 27], "crig": [26, 27], "11326": [26, 27], "vsig4": [26, 27], "v": [26, 27], "immunoglobulin": [26, 27], "domain": [26, 27], "q9y279": [26, 27], "cm_cd163": [26, 27], "cd163": [26, 27], "9332": [26, 27], "molecul": [26, 27, 28], "q86vb7": [26, 27], "found": [26, 28], "suggest": 26, "synonyms_mapp": 26, "inplac": 26, "seen": 26, "were": 26, "among": 26, "channel": 26, "don": 26, "realli": 26, "find": 26, "cell_marker_bionty_lookup": [26, 27], "ccr7": 26, "163": 26, "cm_ccr7": 26, "1236": 26, "motif": 26, "chemokin": 26, "p32248": 26, "inde": 26, "had": 26, "typo": 26, "instead": 26, "help": 26, "elimin": 26, "curated_df": 26, "ok": 26, "again": [26, 28], "cell_type_bionti": [26, 28], "__ratio__": 26, "0000084": 26, "Of": [26, 28], "lymphocyt": 26, "characteri": 26, "0002419": 26, "0000798": 26, "0000789": 26, "0002420": 26, "307692": 26, "By": [26, 27], "nodal": 26, "myocyt": 26, "0002072": 26, "special": 26, "cardiac": 26, "In": [26, 28], "sinoatria": 26, "pacemak": 26, "myocytu": 26, "nodali": 26, "1000409": 26, "1000410": 26, "turn": 26, "off": 26, "pp": 26, "0000696": 26, "That": [26, 28], "And": [26, 28], "pancreat": 26, "pol": 26, "enteroendocrin": 26, "0002680": 26, "result": 26, "000000": 26, "doubl": 26, "posit": 26, "alpha": 26, "beta": 26, "thymocyt": 26, "0000809": 26, "express": [26, 28], "r": 26, "dp": 26, "0002428": 26, "0002430": 26, "0002427": 26, "000242": 26, "pigment": 26, "ciliari": 26, "epitheli": 26, "0002303": 26, "part": [26, 28], "epith": 26, "pe": 26, "gip": 26, "0002278": 26, "duodenum": 26, "jejunu": 26, "k": 26, "714286": 26, "ti": 26, "333333": 26, "b": 26, "0000236": 26, "lineag": 26, "capabl": 26, "0009114": 26, "0001201": 26, "complex": 27, "mani": [27, 28], "even": 27, "here": [27, 28], "show": 27, "ll": 27, "examin": 27, "species_bionti": 27, "scientific_nam": 27, "divis": 27, "taxon_id": 27, "assembli": 27, "assembly_access": 27, "variat": 27, "microarrai": 27, "pan_compara": 27, "peptide_compara": 27, "genome_align": 27, "other_align": 27, "core_db": 27, "species_id": 27, "spini": 27, "chromi": 27, "ncbi_80966": 27, "acanthochromis_polyacanthu": 27, "ensemblvertebr": 27, "80966": 27, "asm210954v1": 27, "gca_002109545": 27, "2018": 27, "2020": 27, "n": 27, "y": 27, "acanthochromis_polyacanthus_core_108_1": 27, "eurasian": 27, "sparrowhawk": 27, "ncbi_211598": 27, "accipiter_nisu": 27, "211598": 27, "accipiter_nisus_ver1": 27, "gca_004320145": 27, "2019": 27, "accipiter_nisus_core_108_1": 27, "giant": 27, "ncbi_9646": 27, "ailuropoda_melanoleuca": 27, "9646": 27, "asm200744v2": 27, "gca_002007445": 27, "ailuropoda_melanoleuca_core_108_2": 27, "yellow": 27, "bill": 27, "parrot": 27, "ncbi_241587": 27, "amazona_collaria": 27, "241587": 27, "asm394721v1": 27, "gca_003947215": 27, "amazona_collaria_core_108_1": 27, "mida": 27, "cichlid": 27, "ncbi_61819": 27, "amphilophus_citrinellu": 27, "61819": 27, "midas_v5": 27, "gca_000751415": 27, "amphilophus_citrinellus_core_108_5": 27, "uniquefi": 27, "append": 27, "__0": 27, "__1": 27, "__2": 27, "species_bionty_lookup": 27, "white_tufted_ear_marmoset": 27, "white": 27, "tuft": 27, "ear": 27, "marmoset": 27, "ncbi_9483": 27, "callithrix_jacchu": 27, "9483": 27, "mcaljac1": 27, "pat": 27, "x": 27, "gca_011100555": 27, "callithrix_jacchus_core_108_1": 27, "pig": 27, "select": 27, "through": 27, "loc": 27, "ncbi_9606": 27, "homo_sapien": 27, "9606": 27, "grch38": 27, "p13": 27, "gca_000001405": 27, "2014": 27, "homo_sapiens_core_108_38": 27, "ncbi_10090": 27, "mus_musculu": 27, "10090": 27, "grcm39": 27, "gca_000001635": 27, "mus_musculus_core_108_39": 27, "ncbi_9823": 27, "sus_scrofa": 27, "9823": 27, "sscrofa11": 27, "gca_000003025": 27, "2021": 27, "sus_scrofa_core_108_111": 27, "next": 27, "choic": 27, "therefor": 27, "retriev": 27, "gene_typ": 27, "hgnc_id": 27, "omim_id": 27, "lzl9xt": 27, "ensg00000210049": 27, "mt": 27, "tf": 27, "mt_trna": 27, "mitochondri": 27, "encod": 27, "trna": 27, "phe": 27, "uuu": 27, "sour": 27, "7481": 27, "mttf": 27, "trnf": 27, "ens107": 27, "ilawa7": 27, "ensg00000211459": 27, "rnr1": 27, "mt_rrna": 27, "rrna": 27, "7470": 27, "mot": 27, "mtrnr1": 27, "xkyeqz": 27, "ensg00000210077": 27, "tv": 27, "val": 27, "gun": 27, "7500": 27, "mttv": 27, "trnv": 27, "jdd2jw": 27, "ensg00000210082": 27, "rnr2": 27, "7471": 27, "hn": 27, "mtrnr2": 27, "j58h9b": 27, "ensg00000209082": 27, "tl1": 27, "leu": 27, "uua": 27, "7490": 27, "mttl1": 27, "trnl1": 27, "tcf7": 27, "20388": 27, "sxcrmq": 27, "ensg00000081059": 27, "protein_cod": 27, "transcript": [27, 28], "acc": 27, "11639": 27, "6932": 27, "189908": 27, "tcf": 27, "between": 27, "isin": 27, "brca1": [27, 28], "17731": 27, "nlereh": 27, "ensg00000139618": 27, "dna": 27, "repair": 27, "symbo": 27, "675": 27, "600185": 27, "brcc2": 27, "facd": 27, "fad": 27, "fad1": 27, "fancd": 27, "xrcc11": 27, "63779": 27, "9fy8yo": 27, "ensg00000012048": 27, "672": 27, "1100": 27, "113705": 27, "brcc1": 27, "fanc": 27, "ppp1r53": 27, "rnf53": 27, "gene_bionty_mous": 27, "mgi_id": 27, "epd98t": 27, "ensmusg00000064336": 27, "phenylalanin": 27, "102487": 27, "rioxa6": 27, "ensmusg00000064337": 27, "102493": 27, "ribosom": 27, "rna": [27, 28], "12srrna": 27, "cmielg": 27, "ensmusg00000064338": 27, "valin": 27, "mg": 27, "102472": 27, "trnav": 27, "dbinna": 27, "ensmusg00000064339": 27, "102492": 27, "16srrna": 27, "ri": 27, "no6nbf": 27, "ensmusg00000064340": 27, "leucin": 27, "102482": 27, "leu_1": 27, "trnrl1": 27, "protein_bionti": 27, "protein_bionty_lookup": 27, "abc_transporter_domain_containing_protein": 27, "197375": 27, "7hevwtc": 27, "q9bv39": 27, "uniprotkb_nam": 27, "q9bv39_human": 27, "abc": 27, "transport": 27, "length": 27, "gene_synonym": 27, "ensembl_transcript_id": 27, "1zrr8wy": 27, "a0a024qz08": 27, "a0a024qz08_human": 27, "intraflagellar": 27, "homolog": 27, "chlamydom": 27, "ift20": 27, "90410": 27, "isoform": 27, "cra_c": 27, "xngxtfu": 27, "a0a024qz86": 27, "a0a024qz86_human": 27, "box": 27, "cra_a": 27, "712": 27, "tbx2": 27, "6909": 27, "x9k8ogk": 27, "a0a024qza8": 27, "a0a024qza8_human": 27, "ec": 27, "976": 27, "epha2": 27, "1969": 27, "8jw9ci4": 27, "a0a024qzb8": 27, "a0a024qzb8_human": 27, "battenin": 27, "438": 27, "cln3": 27, "1201": 27, "nznsa6f": 27, "a0a024qzq1": 27, "a0a024qzq1_human": 27, "sirtuin": 27, "silent": 27, "mate": 27, "regula": 27, "747": 27, "sirt1": 27, "23411": 27, "similarli": 27, "cd45": 27, "cm_cd45": 27, "5788": 27, "ptprc": 27, "phosphatas": 27, "m9mml4": 27, "source_nam": 28, "source_websit": 28, "ftp": 28, "pub": 28, "mysql": 28, "cel": 28, "su": 28, "ea58a1010b7e745702a8397a526b3a33": 28, "9331a6a029cb1863bd0584ab41508df7": 28, "github": 28, "d0655766574e63f3fe5ed56d3c030880": 28, "3f94e22fae4cdde88a555c5cd59c47da": 28, "multi": 28, "anatomi": 28, "c7c958a1ee48fdce146f2c1763eed27": 28, "48": 28, "v3": 28, "3367e9a9ae3dee9113024e5108c49091": 28, "hp": 28, "ceeb3ada771908deef620d74cd8e6b0f": 28, "sub": 28, "geneontologi": 28, "02e2337bb1ab7cc4332ef6acc4cbdfa6": 28, "json": 28, "shown": 28, "0000000": 28, "materi": 28, "anatom": 28, "origin": 28, "0001034": 28, "0000003": 28, "0001061": 28, "0000001": 28, "primari": 28, "cultur": 28, "isol": 28, "unpassag": 28, "nativ": 28, "natur": 28, "whi": 28, "0002371": 28, "0000215": 28, "0010017": 28, "000018": 28, "0000005": 28, "fibroblast": 28, "neural": 28, "crest": 28, "deriv": 28, "deriiv": 28, "neura": 28, "0000006": 28, "neuron": 28, "sensu": 28, "animalia": 28, "0000210": 28, "0000204": 28, "0000198": 28, "100008": 28, "tab": 28, "cell_type_bionty_lookup": 28, "astrocyt": 28, "0000127": 28, "neurogli": 28, "macrogli": 28, "nervou": 28, "largest": 28, "numer": 28, "brain": 28, "spinal": 28, "cord": 28, "star": 28, "irregularli": 28, "shape": 28, "With": 28, "long": 28, "those": 28, "end": 28, "feet": 28, "form": 28, "glial": 28, "limit": 28, "membran": 28, "indirectli": 28, "contribut": 28, "blood": 28, "barrier": 28, "thei": 28, "regul": 28, "extracellular": 28, "ionic": 28, "chemic": 28, "reactiv": 28, "microglia": 28, "respond": 28, "injuri": 28, "glia": 28, "arrai": 28, "0002627": 28, "0012000": 28, "0002603": 28, "0002605": 28, "0002606": 28, "0002604": 28, "0000644": 28, "0002626": 28, "0000683": 28, "0000645": 28, "dtype": 28, "pronto_ontologi": 28, "opt": 28, "hostedtoolcach": 28, "x64": 28, "lib": 28, "python3": 28, "site": 28, "all___cl___2023": 28, "15___celltyp": 28, "similari": 28, "tissue_bionti": 28, "processu": 28, "occurr": 28, "span": 28, "0000104": 28, "0035943": 28, "0000105": 28, "0000002": 28, "uterin": 28, "cervix": 28, "lower": 28, "narrow": 28, "portion": 28, "uteru": 28, "It": 28, "j": 28, "neck": 28, "uteri": 28, "caudal": 28, "segment": 28, "nari": 28, "orific": 28, "olfactori": 28, "0010425": 28, "0005928": 28, "0005931": 28, "0000004": 28, "nose": 28, "vertebr": 28, "consist": 28, "peripher": 28, "nasal": 28, "sac": 28, "chemosensori": 28, "sensori": 28, "0003212": 28, "tissue_bionty_lookup": 28, "kidnei": 28, "0002113": 28, "pair": 28, "urinari": 28, "tract": 28, "urin": 28, "As": 28, "Its": 28, "0004538": 28, "0000081": 28, "0004539": 28, "0000082": 28, "0002120": 28, "0000080": 28, "disease_bionti": 28, "disord": 28, "disposit": 28, "undergo": 28, "patholog": 28, "condit": 28, "0100336": 28, "0700096": 28, "0005583": 28, "adrenocort": 28, "insuffici": 28, "endocrin": 28, "Or": 28, "hormon": 28, "occur": 28, "adren": 28, "hypocortisolemia": 28, "cortico": 28, "0015129": 28, "0043370": 28, "alopecia": 28, "0012551": 28, "0012899": 28, "0007184": 28, "0000009": 28, "inherit": 28, "bleed": 28, "platelet": 28, "0009276": 28, "0008552": 28, "0014386": 28, "0000014": 28, "colorblind": 28, "partial": 28, "0010564": 28, "disease_bionty_lookup": 28, "chronic_kidney_diseas": 28, "0005300": 28, "chronic": 28, "impair": 28, "renal": 28, "secondari": 28, "damag": 28, "persist": 28, "three": 28, "month": 28, "ckd": 28, "failur": 28, "0004375": 28, "0001110": 28, "0024327": 28, "0005016": 28, "0001184": 28, "phenotype_bionti": 28, "0040279": 28, "0012823": 28, "0032443": 28, "000011": 28, "abnorm": 28, "bodi": 28, "height": 28, "deviat": 28, "norm": 28, "respect": 28, "0004322": 28, "0012772": 28, "0000098": 28, "multicyst": 28, "dysplasia": 28, "charact": 28, "dysplast": 28, "kidn": 28, "mode": 28, "pattern": 28, "particular": 28, "genet": 28, "trai": 28, "0001442": 28, "0034335": 28, "0001426": 28, "003434": 28, "autosom": 28, "domin": 28, "observ": 28, "tra": 28, "monoallelic_autosom": 28, "phenotype_bionty_lookup": 28, "abnormal_blood_glucose_concentr": 28, "0011015": 28, "glucos": 28, "concentr": 28, "0001943": 28, "0003074": 28, "additon": 28, "categori": 28, "experi": 28, "instrument": 28, "measur": 28, "readout_bionti": 28, "0011021": 28, "mutat": 28, "carier": 28, "statu": 28, "determin": 28, "presenc": 28, "absenc": 28, "kn": 28, "carrier": 28, "0011022": 28, "0700000": 28, "spatial": 28, "proteom": 28, "assai": 28, "visual": 28, "qua": 28, "0700001": 28, "0700002": 28, "phenocycl": 28, "fusion": 28, "discoveri": 28, "whole": 28, "slide": 28, "autom": 28, "fluidic": 28, "oligonu": 28, "readout_bionty_lookup": 28, "molecular": 28, "single_cell_rna_sequenc": 28, "0008913": 28, "singl": 28, "sequenc": 28, "protocol": 28, "profil": 28, "barcod": 28, "Their": 28, "revers": 28, "amplif": 28, "librari": 28, "seq": 28, "scrna": 28, "transcriptom": 28, "0008441": 28, "0030059": 28, "0005684": 28, "0700003": 28, "0008440": 28, "0700004": 28, "0030060": 28, "0005685": 28, "tumor_s": 28, "0004134": 28, "tumor": 28, "size": 28, "physic": 28, "biologi": 30, "extern": 30}, "objects": {"": [[30, 0, 0, "-", "bionty"]], "bionty": [[0, 1, 1, "", "BFXPipeline"], [1, 1, 1, "", "Bionty"], [2, 1, 1, "", "CellLine"], [3, 1, 1, "", "CellMarker"], [4, 1, 1, "", "CellType"], [5, 1, 1, "", "Disease"], [6, 1, 1, "", "Drug"], [7, 1, 1, "", "Gene"], [8, 4, 1, "", "LOCAL_SOURCES"], [9, 1, 1, "", "Ontology"], [10, 1, 1, "", "Pathway"], [11, 1, 1, "", "Phenotype"], [12, 1, 1, "", "Protein"], [13, 1, 1, "", "Readout"], [14, 1, 1, "", "Species"], [15, 1, 1, "", "Tissue"], [16, 0, 0, "-", "dev"], [18, 5, 1, "", "display_available_sources"], [19, 5, 1, "", "display_currently_used_sources"], [20, 5, 1, "", "reset_sources"]], "bionty.BFXPipeline": [[0, 2, 1, "", "df"], [0, 3, 1, "", "source"], [0, 3, 1, "", "species"], [0, 3, 1, "", "version"]], "bionty.Bionty": [[1, 2, 1, "", "df"], [1, 2, 1, "", "fuzzy_match"], [1, 2, 1, "", "inspect"], [1, 2, 1, "", "lookup"], [1, 2, 1, "", "map_synonyms"], [1, 3, 1, "", "source"], [1, 3, 1, "", "species"], [1, 3, 1, "", "version"]], "bionty.CellLine": [[2, 3, 1, "", "source"], [2, 3, 1, "", "species"], [2, 3, 1, "", "version"]], "bionty.CellMarker": [[3, 2, 1, "", "df"], [3, 3, 1, "", "source"], [3, 3, 1, "", "species"], [3, 3, 1, "", "version"]], "bionty.CellType": [[4, 3, 1, "", "source"], [4, 3, 1, "", "species"], [4, 3, 1, "", "version"]], "bionty.Disease": [[5, 3, 1, "", "source"], [5, 3, 1, "", "species"], [5, 3, 1, "", "version"]], "bionty.Drug": [[6, 3, 1, "", "source"], [6, 3, 1, "", "species"], [6, 3, 1, "", "version"]], "bionty.Gene": [[7, 2, 1, "", "df"], [7, 2, 1, "", "lookup"], [7, 3, 1, "", "source"], [7, 3, 1, "", "species"], [7, 3, 1, "", "version"]], "bionty.Ontology": [[9, 2, 1, "", "get_term"], [9, 2, 1, "", "write_obo"]], "bionty.Pathway": [[10, 3, 1, "", "source"], [10, 3, 1, "", "species"], [10, 3, 1, "", "version"]], "bionty.Phenotype": [[11, 3, 1, "", "source"], [11, 3, 1, "", "species"], [11, 3, 1, "", "version"]], "bionty.Protein": [[12, 2, 1, "", "df"], [12, 3, 1, "", "source"], [12, 3, 1, "", "species"], [12, 3, 1, "", "version"]], "bionty.Readout": [[13, 2, 1, "", "df"], [13, 3, 1, "", "source"], [13, 3, 1, "", "species"], [13, 3, 1, "", "version"]], "bionty.Species": [[14, 2, 1, "", "df"], [14, 3, 1, "", "source"], [14, 3, 1, "", "species"], [14, 3, 1, "", "version"]], "bionty.Tissue": [[15, 3, 1, "", "source"], [15, 3, 1, "", "species"], [15, 3, 1, "", "version"]], "bionty.dev": [[17, 5, 1, "", "ontology_info"]]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "py:data", "5": "py:function"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "data", "Python data"], "5": ["py", "function", "Python function"]}, "titleterms": {"bionti": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29], "bfxpipelin": 0, "celllin": 2, "cellmark": [3, 26], "celltyp": [4, 26], "diseas": [5, 28], "drug": 6, "gene": [7, 26, 27], "local_sourc": 8, "ontologi": [9, 23, 24, 25, 28], "pathwai": 10, "phenotyp": [11, 28], "protein": [12, 27], "readout": [13, 28], "speci": [14, 27], "tissu": [15, 28], "dev": [16, 17], "ontology_info": 17, "display_available_sourc": 18, "display_currently_used_sourc": 19, "reset_sourc": 20, "changelog": 21, "concept": 22, "entiti": [22, 25], "configur": 23, "public": 23, "sourc": [23, 25], "local": 23, "displai": 23, "format": 23, "yaml": 23, "file": 23, "set": 23, "default": 23, "version": 23, "extend": 24, "new": 24, "term": 24, "record": [24, 25, 27], "entit": 24, "basic": 25, "biolog": 25, "out": 25, "box": 25, "instal": 25, "look": [25, 26, 27], "up": [25, 26, 27], "auto": 25, "complet": 25, "inspect": [25, 26], "map": [25, 26], "identifi": [25, 26], "refer": [25, 27, 30], "tabl": [25, 27], "track": 25, "synonym": 26, "standard": 26, "unmap": 26, "name": 26, "via": 26, "fuzzi": 26, "string": 26, "match": 26, "cell": [27, 28], "marker": 27, "lookup": 27, "access": 28, "type": 28}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx": 57}, "alltitles": {"bionty.BFXPipeline": [[0, "bionty-bfxpipeline"]], "bionty.Bionty": [[1, "bionty-bionty"]], "bionty.CellLine": [[2, "bionty-cellline"]], "bionty.CellMarker": [[3, "bionty-cellmarker"]], "bionty.CellType": [[4, "bionty-celltype"]], "bionty.Disease": [[5, "bionty-disease"]], "bionty.Drug": [[6, "bionty-drug"]], "bionty.Gene": [[7, "bionty-gene"]], "bionty.LOCAL_SOURCES": [[8, "bionty-local-sources"]], "bionty.Ontology": [[9, "bionty-ontology"]], "bionty.Pathway": [[10, "bionty-pathway"]], "bionty.Phenotype": [[11, "bionty-phenotype"]], "bionty.Protein": [[12, "bionty-protein"]], "bionty.Readout": [[13, "bionty-readout"]], "bionty.Species": [[14, "bionty-species"]], "bionty.Tissue": [[15, "bionty-tissue"]], "bionty.dev": [[16, "module-bionty.dev"]], "bionty.dev.ontology_info": [[17, "bionty-dev-ontology-info"]], "bionty.display_available_sources": [[18, "bionty-display-available-sources"]], "bionty.display_currently_used_sources": [[19, "bionty-display-currently-used-sources"]], "bionty.reset_sources": [[20, "bionty-reset-sources"]], "Changelog": [[21, "changelog"]], "Concepts": [[22, "concepts"]], "Entity": [[22, "entity"]], "Bionty": [[22, "bionty"], [29, "bionty"]], "Configuration": [[23, "configuration"]], "Public bionty sources": [[23, "public-bionty-sources"]], "Local bionty sources": [[23, "local-bionty-sources"]], "Display sources": [[23, "display-sources"]], "Format of the sources yaml file": [[23, "format-of-the-sources-yaml-file"]], "Setting default ontologies and versions": [[23, "setting-default-ontologies-and-versions"]], "Extend Bionty": [[24, "extend-bionty"]], "New terms and records": [[24, "new-terms-and-records"]], "New ontologies": [[24, "new-ontologies"]], "New entites": [[24, "new-entites"]], "Bionty: Basic biological entities": [[25, "bionty-basic-biological-entities"]], "Out-of-the-box ontologies": [[25, "out-of-the-box-ontologies"]], "Installation": [[25, "installation"]], "Look up ontology records with auto-complete": [[25, "look-up-ontology-records-with-auto-complete"]], "Inspect & map identifiers": [[25, "inspect-map-identifiers"], [26, "inspect-map-identifiers"]], "Reference tables of ontologies": [[25, "reference-tables-of-ontologies"]], "Track ontology sources": [[25, "track-ontology-sources"]], "Inspect and mapping synonyms of gene identifiers": [[26, "inspect-and-mapping-synonyms-of-gene-identifiers"]], "Standardize and look up unmapped CellMarker identifiers": [[26, "standardize-and-look-up-unmapped-cellmarker-identifiers"]], "Map CellType names via fuzzy string matching": [[26, "map-celltype-names-via-fuzzy-string-matching"]], "Look up records of species, gene, protein, cell marker": [[27, "look-up-records-of-species-gene-protein-cell-marker"]], "Species": [[27, "species"]], "Reference table": [[27, "reference-table"]], "Lookup records": [[27, "lookup-records"]], "Gene": [[27, "gene"]], "Protein": [[27, "protein"]], "Cell marker": [[27, "cell-marker"]], "Access ontologies: cell type, tissue, disease, phenotype": [[28, "access-ontologies-cell-type-tissue-disease-phenotype"]], "Cell Type": [[28, "cell-type"]], "Tissue": [[28, "tissue"]], "Disease": [[28, "disease"]], "Phenotype": [[28, "phenotype"]], "Readout": [[28, "readout"]], "Reference": [[30, "module-bionty"]]}, "indexentries": {"bfxpipeline (class in bionty)": [[0, "bionty.BFXPipeline"]], "df() (bionty.bfxpipeline method)": [[0, "bionty.BFXPipeline.df"]], "source (bionty.bfxpipeline attribute)": [[0, "bionty.BFXPipeline.source"]], "species (bionty.bfxpipeline attribute)": [[0, "bionty.BFXPipeline.species"]], "version (bionty.bfxpipeline attribute)": [[0, "bionty.BFXPipeline.version"]], "bionty (class in bionty)": [[1, "bionty.Bionty"]], "df() (bionty.bionty method)": [[1, "bionty.Bionty.df"]], "fuzzy_match() (bionty.bionty method)": [[1, "bionty.Bionty.fuzzy_match"]], "inspect() (bionty.bionty method)": [[1, "bionty.Bionty.inspect"]], "lookup() (bionty.bionty method)": [[1, "bionty.Bionty.lookup"]], "map_synonyms() (bionty.bionty method)": [[1, "bionty.Bionty.map_synonyms"]], "source (bionty.bionty attribute)": [[1, "bionty.Bionty.source"]], "species (bionty.bionty attribute)": [[1, "bionty.Bionty.species"]], "version (bionty.bionty attribute)": [[1, "bionty.Bionty.version"]], "cellline (class in bionty)": [[2, "bionty.CellLine"]], "source (bionty.cellline attribute)": [[2, "bionty.CellLine.source"]], "species (bionty.cellline attribute)": [[2, "bionty.CellLine.species"]], "version (bionty.cellline attribute)": [[2, "bionty.CellLine.version"]], "cellmarker (class in bionty)": [[3, "bionty.CellMarker"]], "df() (bionty.cellmarker method)": [[3, "bionty.CellMarker.df"]], "source (bionty.cellmarker attribute)": [[3, "bionty.CellMarker.source"]], "species (bionty.cellmarker attribute)": [[3, "bionty.CellMarker.species"]], "version (bionty.cellmarker attribute)": [[3, "bionty.CellMarker.version"]], "celltype (class in bionty)": [[4, "bionty.CellType"]], "source (bionty.celltype attribute)": [[4, "bionty.CellType.source"]], "species (bionty.celltype attribute)": [[4, "bionty.CellType.species"]], "version (bionty.celltype attribute)": [[4, "bionty.CellType.version"]], "disease (class in bionty)": [[5, "bionty.Disease"]], "source (bionty.disease attribute)": [[5, "bionty.Disease.source"]], "species (bionty.disease attribute)": [[5, "bionty.Disease.species"]], "version (bionty.disease attribute)": [[5, "bionty.Disease.version"]], "drug (class in bionty)": [[6, "bionty.Drug"]], "source (bionty.drug attribute)": [[6, "bionty.Drug.source"]], "species (bionty.drug attribute)": [[6, "bionty.Drug.species"]], "version (bionty.drug attribute)": [[6, "bionty.Drug.version"]], "gene (class in bionty)": [[7, "bionty.Gene"]], "df() (bionty.gene method)": [[7, "bionty.Gene.df"]], "lookup() (bionty.gene method)": [[7, "bionty.Gene.lookup"]], "source (bionty.gene attribute)": [[7, "bionty.Gene.source"]], "species (bionty.gene attribute)": [[7, "bionty.Gene.species"]], "version (bionty.gene attribute)": [[7, "bionty.Gene.version"]], "local_sources (in module bionty)": [[8, "bionty.LOCAL_SOURCES"]], "ontology (class in bionty)": [[9, "bionty.Ontology"]], "get_term() (bionty.ontology method)": [[9, "bionty.Ontology.get_term"]], "write_obo() (bionty.ontology method)": [[9, "bionty.Ontology.write_obo"]], "pathway (class in bionty)": [[10, "bionty.Pathway"]], "source (bionty.pathway attribute)": [[10, "bionty.Pathway.source"]], "species (bionty.pathway attribute)": [[10, "bionty.Pathway.species"]], "version (bionty.pathway attribute)": [[10, "bionty.Pathway.version"]], "phenotype (class in bionty)": [[11, "bionty.Phenotype"]], "source (bionty.phenotype attribute)": [[11, "bionty.Phenotype.source"]], "species (bionty.phenotype attribute)": [[11, "bionty.Phenotype.species"]], "version (bionty.phenotype attribute)": [[11, "bionty.Phenotype.version"]], "protein (class in bionty)": [[12, "bionty.Protein"]], "df() (bionty.protein method)": [[12, "bionty.Protein.df"]], "source (bionty.protein attribute)": [[12, "bionty.Protein.source"]], "species (bionty.protein attribute)": [[12, "bionty.Protein.species"]], "version (bionty.protein attribute)": [[12, "bionty.Protein.version"]], "readout (class in bionty)": [[13, "bionty.Readout"]], "df() (bionty.readout method)": [[13, "bionty.Readout.df"]], "source (bionty.readout attribute)": [[13, "bionty.Readout.source"]], "species (bionty.readout attribute)": [[13, "bionty.Readout.species"]], "version (bionty.readout attribute)": [[13, "bionty.Readout.version"]], "species (class in bionty)": [[14, "bionty.Species"]], "df() (bionty.species method)": [[14, "bionty.Species.df"]], "source (bionty.species attribute)": [[14, "bionty.Species.source"]], "species (bionty.species attribute)": [[14, "bionty.Species.species"]], "version (bionty.species attribute)": [[14, "bionty.Species.version"]], "tissue (class in bionty)": [[15, "bionty.Tissue"]], "source (bionty.tissue attribute)": [[15, "bionty.Tissue.source"]], "species (bionty.tissue attribute)": [[15, "bionty.Tissue.species"]], "version (bionty.tissue attribute)": [[15, "bionty.Tissue.version"]], "bionty.dev": [[16, "module-bionty.dev"]], "module": [[16, "module-bionty.dev"], [30, "module-bionty"]], "ontology_info() (in module bionty.dev)": [[17, "bionty.dev.ontology_info"]], "display_available_sources() (in module bionty)": [[18, "bionty.display_available_sources"]], "display_currently_used_sources() (in module bionty)": [[19, "bionty.display_currently_used_sources"]], "reset_sources() (in module bionty)": [[20, "bionty.reset_sources"]], "bionty": [[30, "module-bionty"]]}})