Peter Fox Data Science – ITEC/CSCI/ERTH Week 3, September 9, 2014 Data formats, metadata standards, conventions, reading and writing data and information (provenance) Peter Fox Data Science – ITEC/CSCI/ERTH Week 3, September 9, 2014

Contents Assignment on data collection exercise Reading from last week Data formats Metadata standards, conventions, Reading and writing data and information (embedded), where does provenance show up? Next week (data analysis I)

Data Formats We will cover some (not all) ASCII, UTF-8, ISO 8859-1 Self-describing formats Table-driven Markup languages and other web-based Database Graphs Unstructured

ASCII American Standard Code for Information Interchange http://www.webopedia.com/TERM/A/ASCII.html Table of characters http://www.webopedia.com/quick_ref/asciicode.asp ISO-8859-1 (aka ISO Latin 1) is a superset of ASCII – used on the web to represent ‘non-ASCII’ characters Non-printing characters

Example – good or bad? MONTHLY.PLT and MONTHLY

Example – good or bad? MONTHLY.PLT and MONTHLY

Example – good or bad?

Example – good or bad? Where is the data? Where is the provenance? SW48-T0271.asc

Example – good or bad? SW48-T0271.asc

EBCDIC Extended Binary-Coded Decimal Interchange Code IBM 7-bit, 8-bit, 9-bit If someone mentions this just RUN away Seriously, it is okay to convert

Making ASCII more useful Delimited: CSV or tab or (gulp) ASCII space Improves parsing How to handle special characters? How to handle ambiguous delimiters? Moving them in/out of “Excel” for e.g. Templates Encoding strings, e.g. ‘f7.4, c32, i8,f5.3,e9.4’

Reading and writing ASCII Text editor (vi, emacs, wordpad) Dangers exist in applications that add hidden formatting, i.e. characters Even cr, lf (two ASCII characters, non-printable) can often cause major reading and interoperability problems Procedural languages (e.g. C) Interpreted languages (e.g. Perl, Python) Data structures are utilized (e.g. typed arrays, often multidimensional) to provide logical organization to data that is read in, or in preparation for writing it out

Data in “data structures” JSON – JavaScript Object Notation json.org/example {"menu": { "id": "file", "value": "File", "popup": { "menuitem": [ {"value": "New", "onclick": "CreateNewDoc()"}, {"value": "Open", "onclick": "OpenDoc()"}, {"value": "Close", "onclick": "CloseDoc()"} ] } }}

Data in “data structures” JSON – JavaScript Object Notation json.org/example {"menu": { "id": "file", "value": "File", "popup": { "menuitem": [ {"value": "New", "onclick": "CreateNewDoc()"}, {"value": "Open", "onclick": "OpenDoc()"}, {"value": "Close", "onclick": "CloseDoc()"} ] } }} The same text expressed as XML: <menu id="file" value="File"> <popup> <menuitem value="New" onclick="CreateNewDoc()" /> <menuitem value="Open" onclick="OpenDoc()" /> <menuitem value="Close" onclick="CloseDoc()" /> </popup> </menu>

Data in “applications” Increasing trend in storing data in application files, e.g. Excel, .mat (Matlab), .sav (IDL), … What advantages? Ready to use Data structures are provided What problems? Data structures may not match the underlying data representation (model), i.e. information and data may be lost (e.g. float instead of double) Format versions Interoperability – can it be read by another app?

FreeForm 10+ years ago there was an attempt to provide a templated (almost table driven) approach Good homework assignment when you are bored – find out why it was created and what happened to it

Spreadsheets E.g. Excel – import data, Save As csv

Documentation?

CDF Common Data Format The Common Data Format (CDF) is a self-describing data format for the storage and manipulation of scalar and multidimensional data in a platform- and discipline-independent fashion Although CDF has its own internal self describing format, it consists of more than just a data format. CDF is a scientific data management package (known as the "CDF Library") which allows programmers and application developers to manage and manipulate scalar, vector, and multi-dimensional data arrays http://cdf.gsfc.nasa.gov/

CDFML The CDF office realized that scientific progress is often impeded by the lack of, or excessive multiplicity of, available standards for data formats and structures and/or data format translators. In a bid to facilitate and promote data sharing with other data formats, the CDF office has decided to adopt Extensible Markup Language (XML) as a basis for establishing interoperability with other scientific data formats and created CDF Markup Language (CDFML) to describe CDF data and metadata. http://cdf.gsfc.nasa.gov/html/cdf_xml2.html

netCDF Network Common Data Format (and API) Self describing – what does this mean? Variables, dimensions, types, attributes, coordinates nc_dump nc_open nc_inquire nc_dim nc_varget/ put nc_attget/ put

NcML NcML is an XML representation of netCDF metadata, (approximately) the header information one gets from a netCDF file with the "ncdump -h" command. NcML is similar to the netCDF CDL (network Common data form Description Language), except, of course, it uses XML syntax. http://www.unidata.ucar.edu/software/netcdf/ncml/ NetCDF-Java library support - http://www.unidata.ucar.edu/software/netcdf-java/index.html

HDF5 HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format. VERY complex API http://www.hdfgroup.org/HDF5/

HDF4 At its lowest level, HDF is a physical file format for storing scientific data At its highest level, HDF is a collection of utilities and applications for manipulating, viewing, and analyzing data in HDF files Between these levels, HDF is a software library that provides high-level APIs and a low-level data interface http://www.hdfgroup.org/products/hdf4/

HDFEOS A variant of HDF for the Earth Observing System (EOS) http://hdfeos.org/ More under metadata later

HDFEOS Profiles over time

Common Data Model Versus 1.0 combines netCDF and HDF into one model, and API Uses the underlying HDF format representation but uses the netCDF v4 API Simplifies access

FITS FITS stands for `Flexible Image Transport System' and is the standard astronomical data format endorsed by both NASA and the IAU. FITS is much more than an image format (such as JPG or GIF) and is primarily designed to store scientific data sets consisting of multi-dimensional arrays (1-D spectra, 2-D images or 3-D data cubes) and 2-dimensional tables containing rows and columns of data. Many APIs http://heasarc.gsfc.nasa.gov/docs/heasarc/fits.html

TIFF/GeoTIFF Tagged Image File Format 24-bit support http://www.libtiff.org/ GeoTIFF is a public domain metadata standard which allows georeferencing information to be embedded within a TIFF file. The potential additional information includes projections, coordinate systems, ellipsoids, datums, and everything else necessary to establish the exact spatial reference for the file. The GeoTIFF format is fully compliant with TIFF 6.0, so software incapable of reading and interpreting the specialized metadata will still be able to open a GeoTIFF file. From wikipedia pages http://www.gisdevelopment.net/technology/ip/mi03117pf.htm

RDBMS (in one slide) A Relational database management system (RDBMS) is a database management system (DBMS) that is based on the relational model as introduced by E. F. Codd. Most popular commercial and open source databases currently in use are based on the relational model. A short definition of an RDBMS may be a DBMS in which data is stored in the form of tables and the relationship among the data is also stored in the form of tables. From wikipedia mysql

BUFR Binary Universal Form for the Representation of meteorological data (BUFR) is a binary data format maintained by the World Meteorological Organization The latest version is BUFR Edition 4 BUFR Edition 3 is also considered current for operational use http://www.wmo.ch/pages/prog/www/WMOCodes/OperationalCodes.html

BUFR structure A BUFR message is composed of six sections, numbered zero through five. Sections 0, 1 and 5 contain static metadata, mostly for message identification. Section 2 is optional; if used, it may contain arbitrary data in any form wished for by the creator of the message (this is only advisable for local use). Section 3 contains a sequence of so-called descriptors that define the form and contents of the BUFR data product. Section 4 is a bit-stream containing the message's core data and meta-data values as laid out by Section 3.The product description contained in Section 3 can be made sophisticated and non-trivial by the use of replication and/or operator descriptors.

GriB GRIB (GRIdded Binary) is a mathematically concise data format commonly used in meteorology to store historical and forecast weather data Significant amount of software available See wikipedia page for more details

ESML ESML is an interchange technology that enables data (both structural and semantic) interoperability with applications without enforcing a standard format within the Earth science community. Users can write external files using ESML schema to describe the structure of the data file. Applications can utilize the ESML Library to parse this description file and decode the data format. Software developers can build data format independent scientific applications utilizing the ESML technology. Semantic tags can be added to the ESML files by linking different domain ontologies to provide a complete machine understandable data description. ESML description file allows the development of intelligent applications that can now understand and "use" the data.

ESML Earth Science Markup Language http://sourceforge.net/projects/esml/ Schema Editor Library Tutorial Application API - IDL

CSML http://csml.badc.rl.ac.uk/ Climate Science Markup Language CSML is a standards-based data model and GML (Geography Markup Language) application schema for atmospheric and oceanographic data with associated software tools developed at the Rutherford Appleton Laboratory. Java library at: http://csml.badc.rl.ac.uk/java/

CSML Java code ProfileCoverage cov = ...; PrintStream out = ...; // e.g. System.out RecordType rangeType = cov.getRangeType(); out.println("<table>"); for (Record record : cov.getRange()) { // Each Record is a row in the table out.print("<tr>"); for (String memberName : rangeType.getMemberNames()) { // Each member represents a different Phenomenon and // is a column in the table. out.print("<td>" + record.getValue(memberName) + "</td>"); } out.println("</tr>"); out.println("</table>"); If you are generating an HTML table or CSV file from a ProfileCoverage that contains measurements of many phenomena at each vertical coordinate value, you will probably want to access the Coverage's collection of Records as follows:

RDF http://www.w3.org/RDF/ - Resource Description Framework Read the introduction and overview Graph representation and encoding RDF the model and RDF/XML the encoding Many tools, and very good language support Is the foundation of ‘data on the web’, see www.linkeddata.org JSON-LD (JSON for Linked Data) We cover this more in a later class

Break?

Metadata formats Fall into three categories Unstructured and disconnected With the data ‘Close’ to the data See the ASCII example and contrast this with the netCDF example Structure around metadata is very important Vocabulary (constraints) are also very useful We dream of contextual metadata…

Dublin Core DCMI is an open organization engaged in the development of interoperable online metadata standards that support a broad range of purposes and business models. ISO Standard 15836-2003 of February 2003 ANSI/NISO Standard Z39.85-2007 of May 2007 IETF RFC 5013 of August 2007 Metadata element set - http://dublincore.org/documents/dces/ Metadata terms - http://dublincore.org/documents/dcmi-terms/ www.dublincore.org

DC Type Vocabulary - Sect. 7 Collection Dataset Event Image InteractiveResource MovingImage PhysicalObject Service Software Sound StillImage DCMI vo

Dcmi vocabulary model from http://dublincore

METS The METS schema is a standard for encoding descriptive, administrative, and structural metadata regarding objects within a digital library, expressed using the XML schema language of the World Wide Web Consortium. The standard is maintained in the Network Development and MARC Standards Office of the Library of Congress, and is being developed as an initiative of the Digital Library Federation. http://www.loc.gov/standards/mets/

METS example

METS example profile

Time ISO 8601 specifies numeric representations of date and time. helps to avoid confusion in international communication due to different national notations increases the portability of computer user interfaces Good read: http://www.cl.cam.ac.uk/~mgk25/iso-time.html In XML encodings, see xsd:datetime http://www.w3.org/TR/NOTE-datetime http://www.w3.org/TR/xmlschema-2/

ISO 19xxx http://www.geoportal-idec.cat/geoportal/eng/familiaiso.html Is a family of standards *yes real ones* Covers Geospatial Features Many more How to read and write?

Spatial representation ISO 19115:2003 defines the schema required for describing geographic information and services It provides information about the identification, the extent, the quality, the spatial and temporal schema, spatial reference, and distribution of digital geographic data ISO 19115:2003 is applicable to: the cataloguing of datasets, clearinghouse activities, and the full description of datasets geographic datasets, dataset series, and individual geographic features and feature properties. From http://www.iso.org/iso/catalogue_detail.htm?csnumber=26020

Spatial representation ISO 19115:2003 defines mandatory and conditional metadata sections, metadata entities, and metadata elements the minimum set of metadata required to serve the full range of metadata applications (data discovery, determining data fitness for use, data access, data transfer, and use of digital data) optional metadata elements - to allow for a more extensive standard description of geographic data, if required a method for extending metadata to fit specialized needs. Though ISO 19115:2003 is applicable to digital data, its principles can be extended to many other forms of geographic data such as maps, charts, and textual documents as well as non-geographic data. From http://www.iso.org/iso/catalogue_detail.htm?csnumber=26020

Spatial representation ISO 19115-2:2009 extends the existing geographic metadata standard by defining the schema required for describing imagery and gridded data It provides information about the properties of the measuring equipment used to acquire the data, the geometry of the measuring process employed by the equipment, and the production process used to digitize the raw data This extension deals with metadata needed to describe the derivation of geographic information from raw data, including the properties of the measuring system, and the numerical methods and computational procedures used in the derivation The metadata required to address coverage data in general is addressed sufficiently in the general part of ISO 19115.

netCDF+CF netCDF – good but there are NO required attributes or controlled vocabularies In the atmospheric sciences, a group formed to developed COARDS – And then CF – the climate and forecast conventions http://cf-pcmdi.llnl.gov/ The conventions define metadata that provide a definitive description of what the data in each variable represents, and the spatial and temporal properties of the data. This enables users of data from different sources to decide which quantities are comparable, and facilitates building applications with powerful extraction, regridding, and display capabilities.

CF standard names http://cf-pcmdi.llnl.gov/documents/cf-standard-names/ E.g. air_pressure_at_cloud_base (def: cloud_base refers to the base of the lowest cloud, units: Pa) Used in netCDF attribute fields

COARDS http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html Cooperative Ocean/Atmosphere Research Data Service For example, if an oceanographic netCDF file encodes the depth of the surface as 0 and the depth of 1000 meters as 1000 then the axis would use attributes as follows: axis_name:units="meters"; 
axis_name:positive="down"; If, on the other hand, the depth of 1000 meters were represented as -1000 then the value of the positive attribute would have been "up". If the units attribute value is a valid pressure unit the default value of the positive attribute is "down”.

HDFEOS http://eospso.gsfc.nasa.gov/eos_homepage/mission_profiles/docs/mission2.gif This was an effort to add a profile/ convention for NASA use of HDF in the EOS mission A lot of custom library software was built to use it (e.g. the IDL HDFEOS library)

More markup languages GML - Geography Markup Language – developed as a way to standardize geographic representations (to facilitate interoperability) ISO 19136:2007 Stores data and metadata Because it focuses on coordinates, is important as representing structural elements, such as points, lines, polygons used in a specific discipline Features application schema to represent roads, rivers, etc. Is stored statically as well as generated dynamically http://schemas.opengis.net/gml/3.2.1/ http://www.opengeospatial.org/standards/gml

Markup languages KML – Keyhole Markup Language – developed as an interlingua for a specific application, i.e. Google Earth Currently stores data and metadata XML tag and nesting provides for embedding structure and associations between metadata and data Uses other markup languages, e.g. GML Currently, KML 2.2 utilizes certain geometry elements derived from GML 2.1.2. These elements include point, line string, linear ring, and polygon. Can contain links (external) to other content Increasingly is now generated dynamically rather than being a storage format KMZ – compressed version of KML http://www.opengeospatial.org/standards/kml/ http://code.google.com/apis/kml/documentation/

KML model

Provenance – metadata in a given context – think this way Who? What? Where? Why? When? How?

Provenance in this data pipeline Provenance is metadata in context What context? Who you are? What you are asking? What you will use the answer for? As soon as you even think about semantics and knowledge encoding/ representation, knowledge is everywhere…. 20080602 Fox VSTO et al.

At the least Keyword-value pair Obs_start_time=“Mon 1 Sep 2014 19:22:30 EDT” Observer=“Peter Fox”

Provenance standards International standards: ISO lineage (see reading) PROV (reading)

Wire protocols Data Access Protocol (www.opendap.org) Devised as a superset protocol/ data structure so that any data format could be translated into it, serialized and transported over a network (and de-serialized) At present (except caching) data is not stored in DAP ‘format’ We’ll cover this in more detail in a later class

What to do when none exist? ISO 19109 UML and tools….

ISO 19109 ISO 19109:2005(E) defines rules for creating and documenting application schemas, including principles for the definition of features Its scope includes the following conceptual modeling of features and their properties from a universe of discourse definition of application schemas use of the conceptual schema language for application schemas transition from the concepts in the conceptual model to the data types in the application schema integration of standardized schemas from other ISO geographic information standards with the application schema. http://www.iso.org/iso/catalogue_detail.htm?csnumber=39891

Summary and discussion What is in common about the data and metadata formats? Many choices for both – what are the key criteria for choosing? Read and write capability Faithful representation of structure of data Accurate representation of metadata with no (or minimal) loss of information

What is next Assignment 2 on the web today Assignment 1 due today, feedback in preparation for week 5 Next week (Data Analysis I) Reading Data formats: netCDF Metadata resources METS OAI-PMH Protocol for Metadata Harvesting Climate and Forecast (CF) conventions