diff --git a/docs/examples/SAHH_kinetics.ipynb b/docs/examples/SAHH_kinetics.ipynb index ac55366..032f852 100644 --- a/docs/examples/SAHH_kinetics.ipynb +++ b/docs/examples/SAHH_kinetics.ipynb @@ -92,20 +92,6 @@ "cell_type": "code", "execution_count": 2, "metadata": {}, - "outputs": [], - "source": [ - "from mtphandler.molecule import Protein\n", - "\n", - "my_variant = Protein(\n", - " id=\"L191G\",\n", - " name=\"L191G\",\n", - ")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, "outputs": [ { "data": { @@ -144500,7 +144486,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -144542,7 +144528,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -144586,19 +144572,19 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ - "
📍 Assigned 228 initial concentration coditions for ['SAH', 'MhSAHH', 'SIH', 'Hyc', 'MtSAHH', 'BUFFER', 'McSAHH', \n", - "'TmSAHH', 'DTNB', 'TNB'] from data/plate_map_SAHH_kinetics.xlsx to the plate.\n", + "📍 Assigned 228 initial concentration coditions for ['MhSAHH', 'MtSAHH', 'McSAHH', 'SAH', 'DTNB', 'Hyc', 'BUFFER', \n", + "'SIH', 'TmSAHH', 'TNB'] from data/plate_map_SAHH_kinetics.xlsx to the plate.\n", "\n" ], "text/plain": [ - "📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\n", - "\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n" + "📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\n", + "\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n" ] }, "metadata": {}, @@ -144634,7 +144620,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "metadata": {}, "outputs": [ { @@ -144874,7 +144860,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -144914,7 +144900,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 8, "metadata": {}, "outputs": [ { @@ -147682,7 +147668,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ @@ -147717,7 +147703,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 10, "metadata": {}, "outputs": [ { @@ -147748,7 +147734,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -147807,7 +147793,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ diff --git a/docs/examples/data/enzymeml_TmSAHH_SAH.json b/docs/examples/data/enzymeml_TmSAHH_SAH.json index 6b48bbd..1c191ca 100644 --- a/docs/examples/data/enzymeml_TmSAHH_SAH.json +++ b/docs/examples/data/enzymeml_TmSAHH_SAH.json @@ -18,7 +18,7 @@ "exponent": 1, "multiplier": null, "scale": 1.0, - "ld_id": "enzml:BaseUnit/7507fc3b-6f31-4ce7-99e4-3df87993a41c", + "ld_id": "enzml:BaseUnit/085c0609-ab77-4c89-9686-e00e2628535c", "ld_type": [ "enzml:BaseUnit" ], @@ -29,7 +29,7 @@ } } ], - "ld_id": "enzml:UnitDefinition/2d99c27f-949b-40f8-acb9-02e22fd46fc5", + "ld_id": "enzml:UnitDefinition/380763e6-e15c-4f8e-b8a0-4a286d0da22d", "ld_type": [ "OBO:UO_0000000" ], @@ -40,7 +40,7 @@ } }, "constant": true, - "ld_id": "enzml:Vessel/2c2bacab-9361-4a5a-bfc9-25ef526dc2f0", + "ld_id": "enzml:Vessel/42805267-b5a9-4bfe-b348-061d4f044a46", "ld_type": [ "enzml:Vessel", "OBO:OBI_0400081" @@ -69,7 +69,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/4e6f2068-6568-4dc8-8bad-5ca5b43ac58b", + "ld_id": "enzml:Protein/efc8d1cb-4880-4115-9980-f0ae647afa2b", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -107,7 +107,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/7acc8306-c72d-46ef-b880-ab42b59c4d76", + "ld_id": "enzml:Protein/84b031d1-b665-4d92-b783-c50f39095dd7", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -145,7 +145,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/fedc65c2-97f9-40e1-b78a-deef15e47ae8", + "ld_id": "enzml:Protein/2d55f1d7-2376-4fc1-b65e-0261440fc0c4", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -183,7 +183,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/a407c986-a00e-4921-921b-2fc5b25c8314", + "ld_id": "enzml:Protein/abbc1199-549a-4ebb-8040-1873c6ea95f0", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -223,7 +223,7 @@ "inchi": null, "inchikey": null, "references": [], - "ld_id": "enzml:SmallMolecule/014feb9b-1b64-4208-9c73-9bf56f5d1c79", + "ld_id": "enzml:SmallMolecule/f5ddc0d9-cfb3-44ec-876e-17a4eeec3def", "ld_type": [ "enzml:SmallMolecule" ], @@ -413,6 +413,92 @@ "id": "E8", "name": "photometric measurement", "species_data": [ + { + "species_id": "TmSAHH", + "initial": 5.0, + "data_unit": { + "id": null, + "name": "umol / l", + "base_units": [ + { + "kind": "mole", + "exponent": 1, + "multiplier": null, + "scale": -6.0, + "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357", + "ld_type": [ + "md:BaseUnit" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + }, + { + "kind": "litre", + "exponent": -1, + "multiplier": null, + "scale": 1.0, + "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e", + "ld_type": [ + "md:BaseUnit" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + } + ], + "ld_id": "OBO:UO_0000064", + "ld_type": [ + "OBO:UO_0000000" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + }, + "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", + "prepared": 5.0, + "data": [], + "time": [], + "time_unit": { + "id": null, + "name": "s", + "base_units": [ + { + "kind": "second", + "exponent": 1, + "multiplier": 60.0, + "scale": 1.0, + "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160", + "ld_type": [ + "md:BaseUnit" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + } + ], + "ld_id": "OBO:UO_0000031", + "ld_type": [ + "OBO:UO_0000000" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + }, + "is_simulated": false, + "ld_id": "enzml:MeasurementData/2d97c741-c14f-49cd-a02f-84a032d483e0", + "ld_type": [ + "enzml:MeasurementData" + ], + "ld_context": { + "enzml": "http://www.enzymeml.org/v2/", + "schema": "https://schema.org/", + "OBO": "http://purl.obolibrary.org/obo/", + "species_id": { + "@type": "@id" + } + } + }, { "species_id": "BUFFER", "initial": 50.0, @@ -425,7 +511,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56", + "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357", "ld_type": [ "md:BaseUnit" ], @@ -438,7 +524,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666", + "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e", "ld_type": [ "md:BaseUnit" ], @@ -468,7 +554,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0", + "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160", "ld_type": [ "md:BaseUnit" ], @@ -486,7 +572,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/59b2d1e3-d027-4223-b313-c41894965c27", + "ld_id": "enzml:MeasurementData/487ebfd9-6d55-4f0e-897c-d211a2f6dae9", "ld_type": [ "enzml:MeasurementData" ], @@ -511,7 +597,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56", + "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357", "ld_type": [ "md:BaseUnit" ], @@ -524,7 +610,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666", + "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e", "ld_type": [ "md:BaseUnit" ], @@ -1998,7 +2084,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0", + "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160", "ld_type": [ "md:BaseUnit" ], @@ -2016,7 +2102,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/b05df68c-0307-4346-b569-2addc828d601", + "ld_id": "enzml:MeasurementData/97d7bf19-8513-4730-a815-2a84b8ea2625", "ld_type": [ "enzml:MeasurementData" ], @@ -2028,10 +2114,61 @@ "@type": "@id" } } + } + ], + "group_id": "", + "ph": 7.4, + "temperature": 37.04466019417476, + "temperature_unit": { + "id": null, + "name": "Celsius", + "base_units": [ + { + "kind": "celsius", + "exponent": 1, + "multiplier": null, + "scale": 1.0, + "ld_id": "md:BaseUnit/d0bcada3-1c11-4e8f-aa1e-aebc218f6be5", + "ld_type": [ + "md:BaseUnit" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + } + ], + "ld_id": "md:UnitDefinition/6ac5c79a-36fd-4f2c-acba-6ac83b58fdba", + "ld_type": [ + "OBO:UO_0000000" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + }, + "ld_id": "enzml:Measurement/cb1495b3-cd84-4c00-ac7c-4c79c9aa7619", + "ld_type": [ + "enzml:Measurement" + ], + "ld_context": { + "enzml": "http://www.enzymeml.org/v2/", + "schema": "https://schema.org/", + "OBO": "http://purl.obolibrary.org/obo/", + "id": { + "@id": "schema:identifier", + "@type": "@id" }, + "group_id": { + "@type": "@id" + } + } + }, + { + "id": "F8", + "name": "photometric measurement", + "species_data": [ { - "species_id": "TmSAHH", - "initial": 5.0, + "species_id": "Hyc", + "initial": 0.0, "data_unit": { "id": null, "name": "umol / l", @@ -2041,7 +2178,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56", + "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357", "ld_type": [ "md:BaseUnit" ], @@ -2054,7 +2191,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666", + "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e", "ld_type": [ "md:BaseUnit" ], @@ -2072,7 +2209,7 @@ } }, "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", - "prepared": 5.0, + "prepared": 0.0, "data": [], "time": [], "time_unit": { @@ -2084,7 +2221,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0", + "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160", "ld_type": [ "md:BaseUnit" ], @@ -2102,7 +2239,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/af80fcc0-7300-46e6-bf76-b41a8cf3da5e", + "ld_id": "enzml:MeasurementData/1ebd3b14-4e5f-4507-9271-065086d3db7b", "ld_type": [ "enzml:MeasurementData" ], @@ -2114,61 +2251,10 @@ "@type": "@id" } } - } - ], - "group_id": "", - "ph": 7.4, - "temperature": 37.04466019417476, - "temperature_unit": { - "id": null, - "name": "Celsius", - "base_units": [ - { - "kind": "celsius", - "exponent": 1, - "multiplier": null, - "scale": 1.0, - "ld_id": "md:BaseUnit/d6cfa323-be66-4591-84d9-570e831169f8", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - } - ], - "ld_id": "md:UnitDefinition/31f16537-09de-4045-ae55-ad3197ffcb70", - "ld_type": [ - "OBO:UO_0000000" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - "ld_id": "enzml:Measurement/b4be0d27-2224-4ca7-9755-95d9d5616271", - "ld_type": [ - "enzml:Measurement" - ], - "ld_context": { - "enzml": "http://www.enzymeml.org/v2/", - "schema": "https://schema.org/", - "OBO": "http://purl.obolibrary.org/obo/", - "id": { - "@id": "schema:identifier", - "@type": "@id" }, - "group_id": { - "@type": "@id" - } - } - }, - { - "id": "F8", - "name": "photometric measurement", - "species_data": [ { - "species_id": "Hyc", - "initial": 0.0, + "species_id": "TmSAHH", + "initial": 5.0, "data_unit": { "id": null, "name": "umol / l", @@ -2178,7 +2264,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56", + "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357", "ld_type": [ "md:BaseUnit" ], @@ -2191,7 +2277,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666", + "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e", "ld_type": [ "md:BaseUnit" ], @@ -2209,7 +2295,7 @@ } }, "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", - "prepared": 0.0, + "prepared": 5.0, "data": [], "time": [], "time_unit": { @@ -2221,7 +2307,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0", + "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160", "ld_type": [ "md:BaseUnit" ], @@ -2239,7 +2325,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/8924cdaa-a816-4d68-af64-4d40e9074a80", + "ld_id": "enzml:MeasurementData/47fb1524-ca52-4f7a-a04e-8bb7657e8de1", "ld_type": [ "enzml:MeasurementData" ], @@ -2253,8 +2339,8 @@ } }, { - "species_id": "BUFFER", - "initial": 50.0, + "species_id": "DTNB", + "initial": 500.0, "data_unit": { "id": null, "name": "umol / l", @@ -2264,7 +2350,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56", + "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357", "ld_type": [ "md:BaseUnit" ], @@ -2277,7 +2363,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666", + "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e", "ld_type": [ "md:BaseUnit" ], @@ -2295,7 +2381,7 @@ } }, "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", - "prepared": 50.0, + "prepared": 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"md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0", + "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160", "ld_type": [ "md:BaseUnit" ], @@ -11641,7 +11641,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/7a3c944e-98a4-4081-8158-c568833e4c1c", + "ld_id": "enzml:MeasurementData/8e3de43f-f7a1-49a1-9047-3ac9522dd7b6", "ld_type": [ "enzml:MeasurementData" ], @@ -11667,7 +11667,7 @@ "exponent": 1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/d6cfa323-be66-4591-84d9-570e831169f8", + "ld_id": "md:BaseUnit/d0bcada3-1c11-4e8f-aa1e-aebc218f6be5", "ld_type": [ "md:BaseUnit" ], @@ -11676,7 +11676,7 @@ } } ], - "ld_id": "md:UnitDefinition/31f16537-09de-4045-ae55-ad3197ffcb70", + "ld_id": "md:UnitDefinition/6ac5c79a-36fd-4f2c-acba-6ac83b58fdba", "ld_type": [ "OBO:UO_0000000" ], @@ -11684,7 +11684,7 @@ "md": "https://github.com/FAIRChemistry/MTPHandler" } }, - "ld_id": "enzml:Measurement/a1394bfd-038b-413d-aafb-2c28f8a3f465", + "ld_id": "enzml:Measurement/3125d780-d5c9-40c7-9a7f-b4e5ade74f94", "ld_type": [ "enzml:Measurement" ], @@ -11704,7 +11704,7 @@ ], "equations": [], "parameters": [], - "ld_id": "enzml:EnzymeMLDocument/01d7bf76-39ee-42af-987b-2a1b46c13e6a", + "ld_id": "enzml:EnzymeMLDocument/b8f2c4ae-16f4-4816-8450-3d543c6d7af2", "ld_type": [ "enzml:EnzymeMLDocument" ], diff --git a/pyproject.toml b/pyproject.toml index 138f14f..badf906 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "mtphandler" version = "0.2.11" -description = "Tool to work with microtiter plate data." +description = "Python package for processing, enriching, and converting microtiter plate data into standardized EnzymeML time-course data, ready for data science." authors = ["haeussma <83341109+haeussma@users.noreply.github.com>"] license = "MIT License" readme = "README.md"