-
Notifications
You must be signed in to change notification settings - Fork 8
/
Copy pathfair-genomes.tex
265 lines (250 loc) · 11.7 KB
/
fair-genomes.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
\documentclass{article}
\usepackage[utf8]{inputenc}
\begin{document}
\setlength\parindent{0pt}
\textbf{FAIR Genomes metadata schema}
\newline
The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. Version 1.3-SNAPSHOT, 2022-02-28. This model consists of 10 modules that contain 120 metadata elements and 290151 lookups in total (excluding null flavors).
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Nr. of elements \\
\hline
Study & NCIT:C63536 & 9 \\
Personal & NCIT:C90492 & 14 \\
Leaflet and consent form & NCIT:C16468 & 9 \\
Individual consent & NCIT:C16735 & 12 \\
Clinical & NCIT:C25398 & 19 \\
Material & NCIT:C43376 & 17 \\
Sample preparation & OBI:0001902 & 9 \\
Sequencing & EDAM:topic\_3168 & 12 \\
Analysis & EDAM:operation\_2945 & 11 \\
HMD Submission & FG:0000750 & 8 \\
\hline
\end{tabular}
\caption[Module overview]{\label{table:table1} FAIR Genomes metadata schema v1.3-SNAPSHOT overview of all modules.}
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Identifier & OMIABIS:0000006 & UniqueID \\
Name & OMIABIS:0000037 & String \\
Description & OMIABIS:0000036 & Text \\
Inclusion criteria & OBI:0500027 & InclusionCriteria lookup (14 choices) \\
Principal investigator & OMIABIS:0000100 & String \\
Contact information & OMIABIS:0000035 & String \\
Study design & OBI:0500000 & Text \\
Start date & NCIT:C69208 & Date \\
Completion date & NCIT:C142702 & Date \\
\hline
\end{tabular}
\caption[Module: Study]{\label{table:table2} Module: Study. A detailed examination, analysis, or critical inspection of one or multiple subjects designed to discover facts. Ontology: NCIT:C63536. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Personal identifier & NCIT:C164337 & UniqueID \\
Gender identity & MESH:D005783 & GenderIdentity lookup (15 choices) \\
Gender at birth & GSSO:009418 & GenderAtBirth lookup (13 choices) \\
Genotypic sex & PATO:0020000 & GenotypicSex lookup (12 choices) \\
Country of residence & NCIT:C171105 & Countries lookup (249 choices) \\
Ancestry & NCIT:C176763 & Ancestry lookup (305 choices) \\
Country of birth & GENEPIO:0001094 & Countries lookup (249 choices) \\
Year of birth & NCIT:C83164 & Integer \\
Inclusion status & NCIT:C166244 & InclusionStatus lookup (4 choices) \\
Age at death & NCIT:C135383 & Integer \\
Consanguinity & OMIT:0004546 & Boolean \\
Primary affiliated institute & NCIT:C25412 & Institutes lookup (219 choices) \\
Resources in other institutes & NCIT:C19012 & Institutes lookup (219 choices) \\
Participates in study & RO:0000056 & Reference to Study \\
\hline
\end{tabular}
\caption[Module: Personal]{\label{table:table3} Module: Personal. Data, facts or figures about an individual; the set of relevant items would depend on the use case. Ontology: NCIT:C90492. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Leaflet title & DC:title & String \\
Leaflet date & DC:date & Date \\
Leaflet version & DC:hasVersion & String \\
Consent form identifier & DC:identifier & UniqueID \\
Consent form title & DC:title & String \\
Consent form accepted date & DC:dateAccepted & Date \\
Consent form valid until & DC:valid & Date \\
Consent form creator & DC:creator & Institutes lookup (219 choices) \\
Consent form version & DC:hasVersion & String \\
\hline
\end{tabular}
\caption[Module: Leaflet and consent form]{\label{table:table4} Module: Leaflet and consent form. A document explaining all the relevant information to assist an individual in understanding the expectations and risks in making a decision about a procedure. This document is presented to and signed by the individual or guardian. Ontology: NCIT:C16468. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Individual consent identifier & ICO:0000044 & UniqueID \\
Person consenting & IAO:0000136 & Reference to Personal \\
Consent form used & IAO:0000136 & Reference to Leaflet and consent form \\
Collected by & NCIT:C45262 & Institutes lookup (219 choices) \\
Signing date & ICO:0000036 & Date \\
Valid from & DC:valid & Date \\
Valid until & DC:valid & Date \\
Represented by & NCIT:C142600 & RepresentedBy lookup (3 choices) \\
Data use permissions & DUO:0000001 & DataUsePermissions lookup (5 choices) \\
Data use modifiers & DUO:0000017 & DataUseModifiers lookup (23 choices) \\
Data use specification & SIO:000090 & Text \\
Allow recontacting & NCIT:C25737 & Recontacting lookup (3 choices) \\
\hline
\end{tabular}
\caption[Module: Individual consent]{\label{table:table5} Module: Individual consent. Consent given by a patient to a surgical or medical procedure or participation in a study, examination or analysis after achieving an understanding of the relevant medical facts and the risks involved. Ontology: NCIT:C16735. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Clinical identifier & NCIT:C87853 & UniqueID \\
Belongs to person & IAO:0000136 & Reference to Personal \\
Phenotype & NCIT:C16977 & Phenotypes lookup (15802 choices) \\
Unobserved phenotype & HL7:C0442737 & Phenotypes lookup (15802 choices) \\
Phenotypic data available & NCIT:C15783 & DCMITypes lookup (6 choices) \\
Clinical diagnosis & NCIT:C15607 & Diseases lookup (9700 choices) \\
Molecular diagnosis gene & NCIT:C20826 & Genes lookup (19202 choices) \\
Molecular diagnosis other & NCIT:C20826 & Text \\
Age at diagnosis & SNOMEDCT:423493009 & Integer \\
Age at last screening & NCIT:C81258 & Integer \\
Medication & NCIT:C459 & Drugs lookup (5632 choices) \\
Drug regimen & NCIT:C142516 & Text \\
Family members affected & HP:0032320 & FamilyMembers lookup (41 choices) \\
Family members sequenced & NCIT:C79916 & FamilyMembers lookup (41 choices) \\
Medical history & NCIT:C18772 & MedicalHistory lookup (1154 choices) \\
Age of onset & Orphanet:C023 & Integer \\
First contact & LOINC:MTHU048806 & Date \\
Functioning & NCIT:C21007 & Text \\
Material used in diagnosis & SIO:000641 & String \\
\hline
\end{tabular}
\caption[Module: Clinical]{\label{table:table6} Module: Clinical. Findings and circumstances relating to the examination and treatment of a patient. Ontology: NCIT:C25398. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Material identifier & NCIT:C93400 & UniqueID \\
Collected from person & SIO:000244 & Reference to Personal \\
Belongs to diagnosis & SIO:000068 & Reference to Clinical \\
Sampling timestamp & EFO:0000689 & DateTime \\
Registration timestamp & NCIT:C25646 & DateTime \\
Sampling protocol & EFO:0005518 & Text \\
Sampling protocol deviation & NCIT:C50996 & String \\
Reason for sampling protocol deviation & NCIT:C93529 & String \\
Biospecimen type & NCIT:C70713 & BiospecimenTypes lookup (403 choices) \\
Anatomical source & NCIT:C103264 & AnatomicalSources lookup (13827 choices) \\
Pathological state & NCIT:C28257 & PathologicalState lookup (4 choices) \\
Storage conditions & NCIT:C96145 & StorageConditions lookup (26 choices) \\
Expiration date & NCIT:C164516 & Date \\
Percentage tumor cells & NCIT:C127771 & Decimal \\
Physical location & GAZ:00000448 & String \\
Analyses performed & IAO:0000702 & AnalysesPerformed lookup (20 choices) \\
Derived from & NCIT:C28355 & String \\
\hline
\end{tabular}
\caption[Module: Material]{\label{table:table7} Module: Material. A natural substance derived from living organisms such as cells, tissues, proteins, and DNA. Ontology: NCIT:C43376. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Sampleprep identifier & NCIT:C132299 & UniqueID \\
Belongs to material & NCIT:C25683 & Reference to Material \\
Input amount & AFRL:0000010 & Integer \\
Library preparation kit & GENEPIO:0000085 & NGSKits lookup (619 choices) \\
PCR free & NCIT:C17003 & Boolean \\
Target enrichment kit & NCIT:C154307 & NGSKits lookup (619 choices) \\
UMIs present & EFO:0010199 & Boolean \\
Intended insert size & FG:0000001 & Integer \\
Intended read length & NCIT:C153362 & Integer \\
\hline
\end{tabular}
\caption[Module: Sample preparation]{\label{table:table8} Module: Sample preparation. A sample preparation for a nucleic acids sequencing assay. Ontology: OBI:0001902. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Sequencing identifier & NCIT:C171337 & UniqueID \\
Belongs to sample preparation & NCIT:C25683 & Reference to Sample preparation \\
Sequencing date & GENEPIO:0000069 & Date \\
Sequencing platform & GENEPIO:0000071 & SequencingPlatform lookup (7 choices) \\
Sequencing instrument model & GENEPIO:0001921 & SequencingInstrumentModels lookup (45 choices) \\
Sequencing method & FIX:0000704 & SequencingMethods lookup (35 choices) \\
Median read depth & NCIT:C155320 & Integer \\
Observed read length & NCIT:C153362 & Integer \\
Observed insert size & FG:0000002 & Integer \\
Percentage Q30 & GENEPIO:0000089 & Decimal \\
Percentage TR20 & FG:0000003 & Decimal \\
Other quality metrics & EDAM:data\_3914 & Text \\
\hline
\end{tabular}
\caption[Module: Sequencing]{\label{table:table9} Module: Sequencing. The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. Ontology: EDAM:topic\_3168. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Analysis identifier & AFR:0001979 & UniqueID \\
Belongs to sequencing & NCIT:C25683 & Reference to Sequencing \\
Physical data location & GAZ:00000448 & String \\
Abstract data location & NCIT:C142494 & String \\
Data formats stored & NCIT:C142494 & DataFormats lookup (582 choices) \\
Algorithms used & NCIT:C16275 & Text \\
Reference genome used & EDAM:data\_2340 & GenomeAccessions lookup (29 choices) \\
Bioinformatic protocol used & EDAM:data\_2531 & Text \\
Bioinformatic protocol deviation & NCIT:C50996 & String \\
Reason for bioinformatic protocol deviation & NCIT:C93529 & String \\
WGS guideline followed & NCIT:C17564 & String \\
\hline
\end{tabular}
\caption[Module: Analysis]{\label{table:table10} Module: Analysis. An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output. Ontology: EDAM:operation\_2945. }
\end{table}
\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Submitter Role & FG:0000752 & String \\
Data Center & FG:0000753 & String \\
Clinical Center & FG:0000754 & String \\
Institution Clinical & FG:0000755 & InstitutesROR lookup (102392 choices) \\
Institution Data Center & FG:0000756 & InstitutesROR lookup (102392 choices) \\
Publication description & FG:0000757 & String \\
Collection & FG:0000751 & String \\
Research Consortia & FG:0000758 & String \\
\hline
\end{tabular}
\caption[Module: HMD Submission]{\label{table:table11} Module: HMD Submission. A class specific for the 1+MG GDI project containing items for metadata submission. Ontology: FG:0000750. }
\end{table}
\begin{table}[htb]
\begin{tabular}{ll}
Value & Ontology \\
\hline
NoInformation & HL7:NI \\
Invalid & HL7:INV \\
Derived & HL7:DER \\
Other & HL7:OTH \\
Negative infinity & HL7:NINF \\
Positive infinity & HL7:PINF \\
Un-encoded & HL7:UNC \\
Masked & HL7:MSK \\
Not applicable & HL7:NA \\
Unknown & HL7:UNK \\
Asked but unknown & HL7:ASKU \\
Temporarily unavailable & HL7:NAV \\
Not asked & HL7:NASK \\
Not available & HL7:NAVU \\
Sufficient quantity & HL7:QS \\
Trace & HL7:TRC \\
\hline
\end{tabular}
\caption[NullFlavors]{\label{table:table12} Overview of null flavors. Each lookup is supplemented with so-called 'null flavors' from HL7. These can be used to indicate precisely why a particular value could not be entered into the system, providing substantially more insight than simply leaving a field empty. }
\end{table}
\end{document}