Merge pull request #1 from iobis/master

merging main branch

darwin_core.md

@@ -162,7 +162,7 @@ _Data from [Benthic fauna around Franz Josef Land](http://ipt.vliz.be/eurobis/re
 
 `occurrenceStatus` (required term) is a statement about the presence or absence of a taxon at a location. It is an important term, because it allows us to distinguish between presence and absence records. It is a required term and should be filled in with either `present` or `absent`.
 
-A few terms related to quantity: `organismQuantity` and `organismQuantityType`, have been added to the TDWG ratified Darwin Core. This is a lot more versatile than the older `individualCount` field. However, OBIS recommends to use the [Extended MeasurementorFact extension](../data_format/#emof) for quantitative measurements because of the standardization of terms and the fact that you can link these measurements to sampling events and factual sampling information. 
+A few terms related to quantity: `organismQuantity` and `organismQuantityType`, have been added to the TDWG ratified Darwin Core. This is a lot more versatile than the older `individualCount` field. However, OBIS recommends to use the [Extended MeasurementorFact extension](data_format.html#extendedmeasurementorfact-extension-emof) for quantitative measurements because of the standardization of terms and the fact that you can link these measurements to sampling events and factual sampling information. 
 
 Please take note that OBIS recommends all quantitative measurements and sampling facts to be treated in the `ExtendedMeasurementOrFact` extension and not in the Darwin Core files.
 
@@ -236,7 +236,7 @@ The name of the place or location can be provided in `locality`, and if possible
 
 A [Well-Known Text](https://en.wikipedia.org/wiki/Well-known_text) (WKT) representation of the shape of the location can be provided in `footprintWKT`. This is particularly useful for tracks, transects, tows, trawls, habitat extent or when an exact location is not known. WKT strings can be created using our [WKT tool](https://obis.org/maptool). This tool also calculates a midpoint and a radius, which can then be added to `decimalLongitude`, `decimalLatitude`, and `coordinateUncertaintyInMeters` respectively. There is also an [R tool](https://github.com/iobis/obistools#calculate-centroid-and-radius-for-wkt-geometries) to calculate the centroid and radius for WKT polygons. [wktmap.com](https://wktmap.com) can be used to visualize and share WKT strings.
 
-<img src="../images/wkttool2.png" class="img-responsive"/>
+<img src="images/wkttool2.png" class="img-responsive"/>
 
 Some examples of WKT strings:
 

index.Rmd

@@ -4,6 +4,10 @@ site: "bookdown::bookdown_site"
 output:
   bookdown::gitbook:
     split_by: rmd
+    config:
+      toc:
+        before: |
+          <li><a href="/">The OBIS manual</a></li>
 documentclass: book
 biblio-style: apalike
 link-citations: yes

policy.md

@@ -1,15 +1,6 @@
----
-title: Data Policy
-shorttitle: Data policy
-layout: page
-lang: en
-identifier: datapolicy
-breadcrumbs: manual
----
+## Data Policy
 
-# Data Policy
-
-## Guidelines on the sharing and use of data in OBIS
+### Guidelines on the sharing and use of data in OBIS
 
 Adopted at SG-OBIS-IV (Feb 2015) and IODE-XXIII (March 2015).
 
@@ -22,7 +13,7 @@ The OBIS data policy is based on the principles of timely, free and unrestricted
 
 Unless data are collected through activities funded by IOC/IODE, neither UNESCO, IOC, IODE, the OBIS Secretariat, nor its employees or contractors, own the data in OBIS and they take no responsibility for the quality of data or products based on OBIS, or the use or misuse that people may make of them nor can it control or limit the use of any data or products accessible through its website, other than through the use of a published Data Sharing and Use Terms and Conditions.
 
-### Data sharing agreement
+#### Data sharing agreement
 
 The data providers retain all rights and responsibilities associated with the data they make available to OBIS via the OBIS nodes. The OBIS nodes warrant that they have made the necessary agreements with the original data providers that it can make the data available to OBIS data under the following Creative Commons licenses:
 
@@ -40,7 +31,7 @@ The data providers are responsible for the completeness of the data and metadata
 
 In pursuance of copyright compliance, OBIS endeavours to secure permission from rights holders to ingest their datasets. In the event that the inclusion of a dataset in OBIS is challenged on the basis of copyright infringement, OBIS will follow a take-down policy until there is resolution.
 
-### Data use agreement
+#### Data use agreement
 
 The data in OBIS are freely available to everyone, following the principles of equitable access and benefit sharing and supporting capacity development and participation of all IOC Member States in global programmes. However, data users are expected to give attribution to the data providers (see Citations) and the use of data from OBIS should happen in the light of fair use, i.e.:
 
@@ -49,7 +40,7 @@ The data in OBIS are freely available to everyone, following the principles of e
 * In the case you are a custodian of biogeographic data yourself you should take action to also publish these data through OBIS.
 * Consider sponsoring or partnering with OBIS and its OBIS nodes in grant proposal writing. Creating a global database like OBIS cannot happen without the, often voluntary, contribution of many scientists and data managers all over the world. Several activities, such as the coordination, data aggregation, quality control, database and website maintenance require resources including manpower at national and international level. A list of sponsors can be found [here](/about/sponsor)
 
-### Citations
+#### Citations
 
 General OBIS citation:
 
@@ -81,7 +72,7 @@ The derived information products from OBIS are published under the CC-0 license
 OBIS (YEAR) [Information product e.g. Global map showing the Hulbert index in a gridded view of hexagonal cells] [Map] (Available: Ocean Biodiversity Information System. Intergovernmental Oceanographic Commission of UNESCO. www.obis.org. Accessed: YYYY-MM-DD)
 ```
 
-### Disclaimer
+#### Disclaimer
 
 Appropriate caution is necessary in the interpretation of results derived from OBIS. Users must recognize that the analysis and interpretation of data require background knowledge and expertise about marine biodiversity (including ecosystems and taxonomy). Users should be aware of possible errors, including in the use of species names, geo-referencing, data handling, and mapping. They should crosscheck their results for possible errors, and qualify their interpretation of any results accordingly.