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Mapping fields between MBC Autopsy Metadata and HCA metadata

18 November 2019

Zinaida Perova

on behalf of the HCA Metadata Team

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Mapping exercise

2

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Metastatic Breast Cancer Autopsy Metadata

3

Autopsy Worksheet
Fluid Checklist
Soft Tissues
Specimen Metadata
Subject Metadata

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Manual field assessment

4

Good match

Possible match/related field

No match

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Autopsy Worksheet

10 fields

5

Date

Cause of death

Time Autopsy Completed

End time

Time body received in morgue

3

6

1

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Fluid Checklist

7 fields

6

Sample ID

Appearance

Processing date

Start time

Volume

3

1

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Soft Tissues

7 fields

7

Sample ID

Organ code

Fix/storage method

Storage method

Preservation method

Modifiers

5

1

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Specimen Metadata

29 fields

8

Collection site

Date of harvest

Fixative type

Preservation method

Core Body temperature

15

11

3

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Subject Metadata

59 fields

9

Age

Ethnicity

Sex

Asthma status

Diseases

Age at puberty

Breastfeeding history

History of pregnancy

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11

34

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MBC Autopsy worksheet: summary

112 fields

10

Good match

Possible match/related field

No match

40

32

40

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HCA Metadata standard - Motivation

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Data consumers: search and interpret data efficiently and in a standardized way
Tool developers: rely on metadata to develop and implement analysis and visualization tools
Data contributors: describe their project in a useful way

High-quality data
Maximal exploitation by consumers and developers

HCA benefits from being able to adhere to FAIR principles

First, it’s vital that data consumers coming to the HCA are able to efficiently search for data they want and interpret the data they find in an efficient and standardized way. Whether coming to the HCA to retrieve data to supplement their own or to generate testable hypotheses, having a well-defined and accessible metadata standard is key to interpreting the data. Having a well-defined and accessible metadata standard is equally important for those who develop tools or algorithms against the data in the HCA or are using HCA data to populate an analysis or visualization portal. These developers need to be able to control for variation due to batch effects, distinguish between batch effects and variance due to biological factors.

From the other side, those contributing their data to the HCA benefit from having a metadata standard to reference by being assured that what they submit is of high-quality and maximally useful to downstream consumers.

Finally, by requiring data contributors to adhere to the standard and supply the standard to data consumers, the HCA benefits by supporting FAIR principles for data sharing and reuse - that the data are findable within the Atlas, accessible both programmatically and through user interfaces, interoperable with other pieces of software despite being from different labs, and ultimately reusable to extend their use to the scientific community. These principles are especially important for the HCA project given how rapidly the field of cellular resolution biology is evolving.

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Proposed plan

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Masterlist

Ranking

Importance - Contributor’s view

Importance - Consumer’s view

Ease of obtaining

Fields

Use cases

User-friendly format

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Questions and comments

13

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HCA Metadata Standard

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Component	Required fields	Optional fields
Donor and specimen	10	35
Cell line and organoid	5	26
Protocols	1	16
Single cell isolation	4	6
Library construction	5	9
Sequencing assays	3	5
Raw data and sequences	10	4
Project	9	12