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SpecDB/sample/sample_forms/complete_sample.yaml
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| user: # provide information about a user, REQUIRED: `user_id` | |
| 0: | |
| user_id: # no spaces, must be unique, len <= 8, Ex: KJF | |
| given_name: # len <= 64, Ex: Keith | |
| family_name: # len <= 64, Ex: Fraga | |
| middle_initials: # len <= 16, Ex: J | |
| department_and_institution: # len <= 128, Ex: MCB UCD | |
| country: # len <= 32, Ex: USA | |
| state_province: # len <= 32, Ex: NY | |
| city: # len <= 32, Ex: Troy | |
| postal_code: # len <= 32, Ex: 12180 | |
| role: # len <= 64, Ex: postdoc | |
| organization_type: # len <= 64, Ex: academic | |
| email_address: # no spaces, must have `@`, len <= 64, Ex: user@mail.com | |
| project: # provide information describing a project, REQUIRED: `project_id` | |
| 0: | |
| structural_genomics: # not required, only yes or no | |
| project_id: # required, must be unique, no spaces, len <= 32, Ex: SpikeFraga | |
| project_details: # not required, short description, len <= 128, Ex: Spike protein project 2022 | |
| target: # molecular target information, REQUIRED: `target_id` | |
| 0: | |
| target_id: # text identifier for target, must be unique, no spaces, len <= 32, Ex: Db0515 | |
| target_comment: # free field comment, anything to note about target, len <= 128, Ex: from UW-Madison | |
| target_sequence: # target's molecular seq., any type of code/alphabet, no spaces, len <= 1024, Ex: MGSHHHHILVAM | |
| organism_source: # organism name for target source, can indicate if target is synthetic, len <= 128, Ex: synthetic | |
| gene_name: # gene name, len <= 64, Ex: SpikeCoV2 | |
| project_id: # `project_id` target is a member of, must be in project table, Ex: SpikeFraga | |
| target_preparer: # `user_id` that assigned the target, must be in user table, Ex: KJF | |
| construct: # molecular construct from a target, REQUIRED: `construct_id`, | |
| 0: | |
| construct_id: # text identifier for construct, must be unique, no spaces, len <= 32, Ex: Db0515A | |
| construct_sequence: # construct sequence, any type of code/alphabet, no spaces, len <= 1024, Ex: MGSHHHINLVAE | |
| target_id: # `target id` this construct was made for, must already be in target table, Ex: Db0515 | |
| ext_coefficient_280: # extinction coefficient at 280 nm, Ex: 108.7 | |
| expected_mw: # expected molecular weight of construct in Da, Ex: 1211.8 | |
| construct_comment: # free field comment, anything to note about construct, len <= 128, Ex: with primers RE1A/RE1B | |
| plasmid_id: # plasmid construct DNA sequence is cloned in, len <= 64, Ex: pET218(+) | |
| plasmid_id_comment: # comments on plasmid, len <= 256, Ex: from Underwood lab | |
| construct_preparer: # `user_id` who prepared the construct, must already be in user table, Ex: KJF | |
| construct_company: # if the construct was produced by a company, indicate where it came from, len <= 128, Ex: Genscript | |
| expression: # describe a molecular expression experiment/results, REQUIRED: `expression_id` | |
| 0: | |
| expression_id: # text identifier for expression, must be unique, no spaces, len <= 32, Ex: Db0515A.X | |
| expression_comment: # free field comment, anything of note for expression, len <= 128, Ex: reached 4.5 OD | |
| construct_id: # `construct_id` this expression was for, must already be in construct table, Ex: Db0515A | |
| expression_media: # growth media expression was in, len <= 32, Ex: MJ9 | |
| strain: # cellular strain expression was in, len <= 32, Ex: BL21A (+) | |
| expression_organism: # organism expression was in, len <- 32, Ex: E. colli | |
| expression_preparer: # `user_id` of person who did the expression, must already be in user table, Ex: KJF | |
| purification_batch: # describe the purification run for an expression product, REQUIRED: `batch_id` | |
| 0: | |
| batch_id: # text identifier for batch, must be unique, no spaces, len <= 32, Ex: Db0515.X.batch | |
| expression_id: # expression run this purification batch is for, must already be in expression table Ex: Db0515.X | |
| sample_sequence: # sequence of molecule after purification (i.e if there was tag cleaving), any type of code/alphabet, no spaces, len <= 1024, Ex: MQNGPILA | |
| purif_comment: # free text comment about the purification, len <= 128, Ex: HPLC in RM 204 | |
| production_method: # indicate the purification method, len <= 64, Ex: Ni column only | |
| isotopic_labeling_remark: # provide the isotopic labeling, preferred method to indicate labeling in the appropriate column below, len <= 64, Ex: NC5 | |
| iso_13c_enrichment: # 13C labeling percentage, must contain `% 13C`, len <= 32, Ex: 100% 13C | |
| iso_15n_enrichment: # 15N labeling percentage, must contain `% 15N`, len <= 32, Ex: 99% 15N | |
| iso_2h_enrichment: # 2H labeling percentage, must contain `% 2H`, len <= 32, Ex: 100% 2H | |
| iso_19f_Trp_enrichment: # 19F-Trp labeling percentage, must contain `% 19F-Trp`, len <= 32, Ex: 11% 19F-Trp | |
| iso_19f_Phe_enrichment: # 19F-Phe labeling percentage, must contain `% 19F-Phe`, len <= 32, Ex: 9.1% 19F-Phe | |
| iso_1hd1_Leu_methyl_enrichment: # 1HD1-Leu stereospecific labeling percentage, must contain `% 1HD1-Leu`, len <= 32, Ex: 13.3% 1HD1-Leu | |
| iso_1hd2_Leu_methyl_enrichment: # 1HD2-Leu stereospecific labeling percentage, must contain `% 1HD2-Leu`, len <= 32, Ex: 15% 1HD2-Leu | |
| iso_1hd_Ile_methyl_enrichment: # 1HD-Ile labeling percentage, must contain `% 1HD-Ile`, len <= 32, Ex: 50% 1HD-Ile | |
| iso_1hg1_Val_methyl_enrichment: # 1HG1-Val stererospecific labeling percentage, must contain `% 1HG1-Val`, len <= 32, Ex: 25% 1HG1-Val | |
| iso_1hg2_Val_methyl_enrichment: # 1HG2-Val stereospecific labeling percentage, must contain `% 1HG2-Val`, len <= 32, Ex: 27%% 1HG2-Val | |
| iso_1hb_Ala_methyl_enrichment: # 1HB-Ala labeling percentage, must contain `% 1HB-Ala`, len <= 32, Ex: 100% 1HB-Ala | |
| batch_preparer: # `user_id` of person who did the purification, must already be in user table, Ex: KJF | |
| buffer: # store all buffers used, their id and their pH, REQUIRED: `buffer_id`, `buffer_pH`, NOTE: the buffer components go in the `buffer_components` table | |
| 0: | |
| buffer_id: # text identifier for the buffer, must be unique, no spaces, len <= 32, Ex: hn4071 | |
| buffer_ph: # pH of buffer, must be a number, Ex: 8.1 | |
| buffer_comment: # free text field for any notes about the buffer, len <= 128, Ex: made by KJF 12/04 | |
| buffer_components: # describe the component(s) of a buffer, REQUIRED: `buffer_id`, `buffer_component`, `buffer_component_value`, `buffer_component_unit` | |
| 0: | |
| buffer_id: # `buffer_id` this component goes to, must already be in buffer table, Ex: hn4071 | |
| buffer_component: # name of the component, len <= 64, Ex: NaCl | |
| buffer_component_value: # the numeric concentration value of the component, Ex: 100.0 | |
| buffer_component_unit: # unit of concentration, one of (`mM`, `% (v/v)`, `mg/mL`), Ex: mM | |
| pst: # description of a protein sample tube, not only proteins, REQUIRED: `pst_id`, `pst_preparer`, `sample_ph`, `total_volume`, `volume_unit`, `tube_type` | |
| 0: | |
| pst_id: # text identifier for the pst, must be unique, no spaces, len <= 32, Ex: Db0515A.001 | |
| prev_pst_id: # if pst derived from another pst, give previous `pst_id`, must already be in pst table, Ex: Db0515A.000 | |
| pst_preparer: # `user_id` of user that prepared the sample tube, must be in user table, Ex: KJF | |
| pst_comment: # free field comment about pst, len <= 128, Ex: new sample | |
| sample_type: # is sample a solution or solid-state sample, one of (`solution`, `solid state`), Ex: solution | |
| solvent_system: # solvent system for the sample, len <= 64, Ex: DMSO | |
| sample_ph: # pst pH, can be different from buffer ph, Ex: 7.1 | |
| total_volume: # numeric volume for total volume in tube, Ex: 2.2 | |
| volume_unit: # unit of volume for volume in tube, one of (`nL`, `uL`, `mL`, `L`), Ex: mL | |
| curr_location: # current location of tube, len <= 64, Ex: NMR room | |
| prev_location: # previous location of tube, len <= 64, Ex: Underwood lab | |
| create_date: # date record added to database, format "YYYY-MM-DD", Ex: 2022-01-01 | |
| buffer_id: # id of buffer in the tube, must already be in `buffer` table, no spaces, len <= 32, Ex: hn4071 | |
| tube_type: # the tube type for sample tube, use `specdb summary --table tubes` to find allowable tube types, Ex: 1-mm Shigemi tube | |
| batch_components: # describe the purification batches in a pst, REQUIRED: `pst_id`, `batch_id`, `volume`, `volume_unit`, `conc`, `conc_unit` | |
| 0: | |
| pst_id: # text id of sample tube being described, must already be in pst table, Ex: Db0515A.001 | |
| batch_id: # text id of batch in the `pst_id` above, must already be in purification_batch table, Ex: Db0515A.X.batch | |
| conc: # concentration of sample in the sample tube, numeric, Ex: 10.2 | |
| conc_unit: # concentration units, one of (`ug/mL`, `mg/mL`, `nM`, `uM`, `mM`), Ex: mM | |
| mass: # mg of protein sample in tube, Ex: 101.1 | |