Create a flow chart for passive acoustic monitoring data

[MathewBiddle]

Initial attempt at visualizing what is documented at https://www.ncei.noaa.gov/products/passive-acoustic-data#tab-3561

%%{
  init: {
    'theme': 'base',
    'themeVariables': {
      'primaryColor': '#007396',
      'primaryTextColor': '#fff',
      'primaryBorderColor': '#003087',
      'lineColor': '#003087',
      'secondaryColor': '#007396',
      'tertiaryColor': '#CCD1D1'
    },
   'flowchart': { 'curve': 'basis' }
  }
}%%

flowchart TD

A["hydrophone"] 

B{{"PassivePacker"}}

C{{"Darwin Core
Alignment"}}

D[("NCEI")]

E[("IPT
OBIS-USA")]

F[/"MBON 
Data Portal"\]

G([OBIS])

H([GBIF])

P[(IOOS RA ERDDAP)]

I(["IOOS Data Catalog
(data.ioos.us)"])

J([NOAA OneStop])

K([data.gov])

L(["Commerce
Data Hub"])

M[/"IOC-UNESCO Harmful Algae Information System"\]

N[/"Infographics"\]

%% O["GitHub /
%% protocols.io"]


A -- Species Detections --> C
A --raw audio files & 1-min hybrid millidecade bands --> B
B --> D
%% A -- Protocols --> O
C --> E
E --> D
%% O .-> E
E --> G
E --> H

%% NOAA STUFF
%% A -- Environmental Observations --> D
A -- non-acoustic data --> P
P --> I
P -- raw --> D
P -- occurrence --> C
I --> J
I --> K
I --> L
D --> J
D --> K
D --> L

G .-> Q
H .-> Q
F .-> Q
D .-> Q
J .-> Q
K .-> Q
L .-> Q

subgraph Q[Example Products]
M
N
F
end

click C "https://doi.org/10.35035/doc-vf1a-nr22" "GBIF eDNA Manual" _blank
click D "https://www.ncei.noaa.gov" "NCEI" _blank
click F "https://mbon.ioos.us" "MBON" _blank
click G "https://obis.org" "OBIS" _blank
click H "https://gbif.org" "GBIF" _blank
%%click I "https://data.ioos.us" "IOOS Catalog" _blank
%%click J "https://data.noaa.gov/onestop/" "NOAA OneStop" _blank
%%click K "https://data.gov" "data.gov" _blank

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non-acoustic data is essentially anything measured in concert with the passive acoustic hydrophone. For example, abiotic measurements from sensors attached to the same platform, biotic observations nearby (camera trap), etc.

[MathewBiddle]

FYI @ioos/pamdata

[MathewBiddle]

Loosely based on the initial biological data flow at #40 (comment)

[MathewBiddle]

Update to include sound propagation piece.

%%{
  init: {
    'theme': 'base',
    'themeVariables': {
      'primaryColor': '#007396',
      'primaryTextColor': '#fff',
      'primaryBorderColor': '#003087',
      'lineColor': '#003087',
      'secondaryColor': '#007396',
      'tertiaryColor': '#CCD1D1'
    },
   'flowchart': { 'curve': 'basis' }
  }
}%%

flowchart TD

A["hydrophone"] 



B{{"PassivePacker"}}

C{{"Darwin Core
Alignment"}}

D[("NCEI")]

E[("IPT
OBIS-USA")]

F[/"MBON 
Data Portal"\]

G([OBIS])

H([GBIF])

P[(IOOS RA ERDDAP)]

I(["IOOS Data Catalog
(data.ioos.us)"])

J([NOAA OneStop])

K([data.gov])

L(["Commerce
Data Hub"])

M[/"IOC-UNESCO Harmful Algae Information System"\]

N[/"Infographics"\]

%% O["GitHub /
%% protocols.io"]

R[/"NCEI Passive Acoustic Data Portal"\]

A -- Species Detections + sound propagation--> C
A --raw audio files & 1-min hybrid millidecade bands --> B
B --> D
%% A -- Protocols --> O
C --> E
E --> D
%% O .-> E
E --> G
E --> H

%% NOAA STUFF
%% A -- Environmental Observations --> D
A -- non-acoustic data --> P
P --> I
P -- raw --> D
P -- occurrence --> C
I --> J
I --> K
I --> L
D --> J
D --> K
D --> L

G .-> Q
H .-> Q
F .-> Q
D .-> Q
J .-> Q
K .-> Q
L .-> Q

D --> R

subgraph Q[Example Products]
M
N
F
end

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[MathewBiddle]

%%{
  init: {
    'theme': 'base',
    'themeVariables': {
      'primaryColor': '#007396',
      'primaryTextColor': '#fff',
      'primaryBorderColor': '#003087',
      'lineColor': '#003087',
      'secondaryColor': '#007396',
      'tertiaryColor': '#CCD1D1'
    },
   'flowchart': { 'curve': 'basis' }
  }
}%%

flowchart TD

pA(("passive\nacoustic\nmonitoring"))

A[("hydrophone")]

B{{"PassivePacker"}}

C{{"Darwin Core
Alignment"}}

D[("National Centers\nfor\nEnvironmental Information\n(NCEI)")]

E[("IPT
OBIS-USA")]

F[/"MBON 
Data Portal"\]

G([OBIS])

H([GBIF])

%%P[(IOOS RA ERDDAP)]

%%I(["IOOS Data Catalog
%%(data.ioos.us)"])

J([NOAA OneStop])

K([data.gov])

L(["Commerce
Data Hub"])

M[/"IOC-UNESCO Harmful Algae Information System"\]

N[/"Infographics"\]

%% O["GitHub /
%% protocols.io"]

R[/"NCEI Passive Acoustic Data Portal"\]


pA --> A
A -- species detections\n+\nsound propagation--> C
A -- raw\nand\nprocessed\ndata --> B
B --> D
%% A -- Protocols --> O
C --> E
E --> D
%% O .-> E
E --> G
E --> H

%% NOAA STUFF
%% A -- Environmental Observations --> D
%%pA -- non-acoustic data --> P
%%P --> I
%%P -- raw --> D
%%P -- occurrence --> C
%%I --> J
%%I --> K
%%I --> L
D --> J
D --> K
D --> L

G --> D

G .-> Q
H .-> Q
F .-> Q
D .-> Q
J .-> Q
K .-> Q
L .-> Q

D --> R

subgraph Q[Example Products]
M
N
F
R
end

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[MathewBiddle]

Cleaning up some of the nuances in the diagram. Grouping federal catalogs, and example products.

%%{
  init: {
    'theme': 'base',
    'themeVariables': {
      'primaryColor': '#007396',
      'primaryTextColor': '#fff',
      'primaryBorderColor': '#003087',
      'lineColor': '#003087',
      'secondaryColor': '#007396',
      'tertiaryColor': '#CCD1D1'
    },
   'flowchart': { 'curve': 'basis' }
  }
}%%

flowchart TD

pA(("passive\nacoustic\nmonitoring"))

A[("hydrophone")]

B{{"PassivePacker"}}

C{{"Darwin Core
Alignment"}}

D[("National Centers\nfor\nEnvironmental Information\n(NCEI)")]

E[("IPT
OBIS-USA")]

F[/"MBON 
Data Portal"\]

G([OBIS])

H([GBIF])

J([NOAA OneStop])

K([data.gov])

L(["Commerce
Data Hub"])


M[/"IOC-UNESCO Harmful Algae Information System"\]
N[/"Infographics"\]
R[/"NCEI Passive Acoustic Data Portal"\]


pA --> A
A -- species detections\n+\nsound propagation--> C
A -- raw\nand\nprocessed\ndata --> B
C --> E
E --> D
E --> G
E --> H
B --> D

D --> FC

G .-> EP
H .-> EP
D .-> EP

D --> R

FC .-> EP

subgraph EP [Example Products]
M
N
F
R
end

subgraph FC [Federal Catalogs]
J
K
L
end

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[MathewBiddle]

further defining raw and processed data:

Audio, sound level metrics (beyond 1 minute hybrid millidecade, standard metric), detections, sound propagation models, and well organized sound clips

[carriecwall]

The revised version looks much better! And defining processed data is super helpful. Could we make the line from OBIS to NCEI a dashed line since that pathway is not fully defined yet?

[MathewBiddle]

Thanks for taking a look. The pipeline between OBIS-USA's IPT and NCEI is fully operational. See https://www.ncei.noaa.gov/news/archiving-ocean-biodiversity-information-system-usa-obis-usa. The archive package can be found at https://www.ncei.noaa.gov/metadata/geoportal/rest/metadata/item/gov.noaa.nodc%3A0250940/html.

For reference, the Sanctuary Soundscape Monitoring Project (SanctSound) Daily Aggregated Species Detections have been archived via this pathway, from the most recent quarterly pull, at https://www.nodc.noaa.gov/archive/arc0199/0250940/6.6/data/0-data/noaa_sanctsound_daily_species/