MInAS-pathogen

	A	H	L	M
1	item is mandatory (M), conditional mandatory (C), optional (X), environment-dependent (E) or not applicable (-)
2	Structured comment name	MINAS - pathogen	MINAS - pathogen Comment I	MINAS - pathogen Comment II
3	samp_name	M
4	samp_taxon_id	C/X	Problem: SG and capture data contain many microbes, not just studied microbe
5	project_name	M
6	lat_lon	C	Condition: excavation/recovery coordinates known
7	depth	C	Condition: excavation/recovery depth known
8	elev	C	Condition: excavation/recovery coordinates known
9	temp	C	Modified meaning: storage temperature and duration	Condition: storage temperature and duration known
10	geo_loc_name	M
11	collection_date	C/X	Problem: need excavation and collection date; timestamp format not applicable to many excavations
12	neg_cont_type	C	Condition: use of negative control
13	pos_cont_type	C/X	Condition: use of positive control
14	env_broad_scale	C/X	Condition: coordinates known	Problem: landscapes change through time
15	env_local_scale	C/X	Guidance: anatomical site sampled
16	env_medium	C/X	Modified meaning: burial environment (exp. directly interred, stone tomb, cave)
17	subspecf_gen_lin	C	Problem: SG and capture data contain many microbes, not just studied microbe
18	ploidy	C/X	Problem: SG and capture data contain many microbes, not just studied microbe
19	num_replicons	X	Problem: SG and capture data contain many microbes, not just studied microbe
20	extrachrom_elements	X	Problem: SG and capture data contain many microbes, not just studied microbe
21	ref_biomaterial	C	Condition: sample has been sequenced before
22	source_mat_id	M	Guidance: archaeological or museum ID
23	specific_host	M
24	host_disease_stat	X	Problem: decide if this should refer to skeleton pathology or all pathogen hits in the data
25	samp_collec_method	M	Guidance: DOI or description of sampling method; be mindful of replicate protocol fields
26	samp_vol_we_dna_ext	M	Guidance: mass of tissue used for extraction
27	virus_enrich_appr	?	Modified meaning: any enrichment approached used on dataset, not just for viruses
28	nucl_acid_ext	M
29	nucl_acid_amp	C	Condition: PCR-based study
30	lib_reads_seqd	M	Guidance: number of reads sequenced, not clones
31	lib_layout	M
32	lib_screen	M	Question: there is already a field for this in general upload. Do we need duplicate entries?
33	target_gene	C	Condition: PCR-based study
34	target_subfragment	C	Condition: PCR-based study
35	pcr_primers	C	Condition: PCR-based study
36	mid	X
37	adapters	X
38	pcr_cond	C	Condition: PCR-based study
39	seq_meth	M
40	chimera_check	C	Condition: performed chimera assessment
41	tax_ident	X
42	assembly_qual	C	Condition: assembly data
43	assembly_name	C	Condition: assembly data
44	assembly_software	C	Condition: assembly data
45	annot	X/C	Condition: annotated assembly
46	number_contig	C	Condition: assembly data
47	feat_pred	X/C	Condition: assembly data
48	ref_db	X/C	Condition: assembly data
49	sim_search_meth	X/C	Condition: assembly data
50	tax_class	X/C	Problem: results of taxonomic classification are not observable in raw data upload; is this a necessary field?
51	16s_recover	X/C	Condition: 16S rRNA data
52	16s_recover_software	X/C	Condition: 16S rRNA data	Problem: results of analysis are not observable in raw data upload
53	compl_score	X/C	Problem: results of analysis are not observable in raw data upload
54	compl_software	X/C	Problem: results of analysis are not observable in raw data upload
55	compl_appr	X/C	Problem: results of analysis are not observable in raw data upload
56	contam_score	X/C	Problem: results of analysis are not observable in raw data upload
57	contam_screen_input	X/C	Problem: results of analysis are not observable in raw data upload
58	contam_screen_param	X/C	Problem: results of analysis are not observable in raw data upload
59	decontam_software	X/C	Problem: results of analysis are not observable in raw data upload
60	bin_param	C	Condition: performed taxonomic binning	Problem: results of analysis are not observable in raw data upload
61	bin_software	C	Condition: performed taxonomic binning	Problem: results of analysis are not observable in raw data upload
62	reassembly_bin	C	Condition: performed taxonomic binning	Problem: results of analysis are not observable in raw data upload
63	mag_cov_software	C	Condition: performed taxonomic binning	Problem: results of analysis are not observable in raw data upload
64	otu_class_appr	X	Problem: results of analysis are not observable in raw data upload
65	otu_seq_comp_appr	X	Problem: results of analysis are not observable in raw data upload
66	otu_db	X	Problem: results of analysis are not observable in raw data upload
67	associated resource	X
68	sop	C	Condition: assembly data	Problem: results of analysis are not observable in raw data upload
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